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{{ template.Protein{ leadContact:"", title:"Crystal structure of Uncharacterized peroxidase-related protein (YP_604910.1) from Deinococcus geothermalis DSM 11300 at 1.51 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-02-22", targetid:"371529", pdbid:"2oyo", source:"Deinococcus geothermalis dsm 11300", relatedPDBs:[], refids:"YP_604910.1", molwt:"21690.49", residues:"195", isopoint:"5.60", sequence:"mtttqpeakdrisslpvpdatqvpegvrklwakaeanigfvpnvfraqavngeqflawwnyfnlllnkeg yltnaerelvavvvsgvnrclycavshgaalreflgdpqkadavavnwrhadltereqalaayaekltr hpaevtaadleplravglddhqimelvqvigmfnltnrvssalgfvpnpeyyrqar", method:"XRAY", numchains:"2", resolution:"1.51", rfree:"0.215", mattcoeff:"2.38", rfactor:"0.182", waters:"441", solcontent:"48.41", ligands:"MPD ((4S)-2-METHYL-2,4-PENTANEDIOL) x 3", metals:"", model:"False", uniprot:"Q1IYE3_DEIGD", pubmed:"" } }}

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YP_604910.1 is a single domain 195 residues long protein showing the signature of the Carboxy-Mucono-lactone Decarboxylase (CMD) family from positions 50 to 135 with a highly conserved C90-C93-H97 motif (PF02627). Based on the genome context where its gene is located, STRING gives a 0.65 score to the possible functional partner PF04306, a putative membrane protein.

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SCOP classifies 2oyo as belonging to the all alpha class, AhpD-like superfamily, Atu0492-like family. FFAS and HHpred provide the closely related 2pfx as top hit, followed by 2prr and 3c1l, all uncharacterized peroxidase-related proteins. The secondary structure matching server gives a 91% and 82% score to 2prr and 3c1l, respectively.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of flavin reductase domain protein (YP_831077.1) from Arthrobacter sp. FB24 at 1.90 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-06-19", targetid:"375018", pdbid:"2qck", source:"Arthrobacter sp. fb24", relatedPDBs:[], refids:"ARTH_26JUL04_CONTIG32_REVISED_GENE887", molwt:"18262.58", residues:"166", isopoint:"5.28", sequence:"vtsdnaafegtfkemfrrhaagvaiitvnyngtpygftatsvaslsaqpprftfnmarsssswpaiantt higvhmlgldnqeladrfartknrfegdhwelgpyevpilkdvagwligkiqmrlsfennavvvvevve gqvgedgtpllyhsgaysqpvpldyei", method:"XRAY", numchains:"1", resolution:"1.90", rfree:"0.251", mattcoeff:"2.58", rfactor:"0.204", waters:"63", solcontent:"52.26", ligands:"PO4 (PHOSPHATE) x 1", metals:"", model:"False", uniprot:"A0JVA7_ARTS2", pubmed:"" } }}

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The gene Arth_1583 from Arthrobacter sp. FB24 encodes for a flavin reductase (PF01613, cl00801), an enzyme that catalyzes the reduction of FMN (or FAD) using NAD(P)H. The asymmetric unit contains a single copy of the protein which is functional as a dimer. The structure adopts a beta roll (2qck-CATH) and contains a single domain. Similar protein structures derived by PSI include 1eje and 3e4v. See the latter for a detailed description.

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{{ template.Protein{ leadContact:"", title:"Nuclear magnetic resonance structure of the N-terminal domain of nonstructural protein 3 from the severe acute respiratory syndrome coronavirus. 2007",site:'JCSG', status:'In PDB', date:"2006-04-24", targetid:"355891", pdbid:"2gri", source:"Sars coronavirus tor2 isolate", relatedPDBs:["2idy"], refids:"29837497", molwt:"12639.45", residues:"112", isopoint:"4.10", sequence:"apikgvtfgedtvwevqgyknvritfeldervdkvlnekcsvytvesgtevtefacvvaeavvktlqpvs dlltnmgidldewsvatfylfddageenfssrmycsfyppde", method:"NMR", numchains:"1", resolution:"not", rfree:"", mattcoeff:"", rfactor:"", waters:"", solcontent:"", ligands:"", metals:"", model:"False", uniprot:"R1AB_CVHSA", pubmed:"17728234" } }}

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The gene 29837497 from SARS coronavirus encodes the N-terminal domain of nonstructural protein 3 (nsp3a). The protein belongs to the class of alpha and beta proteins (a+b) and reveals beta-Grasp (ubiquitine-like) fold type SCOP. The NMR structure of the same protein has been previously determined 2IDY. In addition to the four beta-strands and two alpha-helices that are common to ubiquitin-like folds, the globular domain of nsp3a contains two short helices representing a new feature of this protein. NMR chemical shift perturbations showed that these unique structural elements are involved in interactions with single-stranded RNA [Ref]. The nsp3a homologue from rotovirus has been shown to bind to 3'-end of viral mRNA during viral infection [Ref]. While bound to mRNA nsp3a interacts with eukaryotic initiation factor 4GI (eIF4GI), displacing its normal partner PABP. This interaction effectively shut offs the cellular protein synthesis, dedicating resources to the viral protein synthesis. Thus, SARS nsp3a seems to have similar function.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of choline/ethanolamine kinase family protein (NP_106042.1) from MESORHIZOBIUM LOTI at 2.55 A resolution. ",site:'JCSG', status:'In PDB', date:"2008-07-24", targetid:"386994", pdbid:"3dxq", source:"Mesorhizobium loti", relatedPDBs:[], refids:"NP_106042.1", molwt:"32971.98", residues:"300", isopoint:"5.76", sequence:"mmtdearaklaaipmlagytgplerlggltnlvfragdlclripgkgteeyinraneavaareaakagvs pevlhvdpatgvmvtryiagaqtmspekfktrpgsparageafrklhgsgavfpfrfelfamiddylkv lstknvtlpagyhdvvreaggvrsalaahplplaachcdplcenfldtgermwivdweysgmndplwdl gdlsvegkfnanqdeelmrayfggearpaergrvviykamcdllwtlwgliqlandnpvddfrayadgr farckalmetpefsrhlaavrmg", method:"XRAY", numchains:"2", resolution:"2.55", rfree:"0.284", mattcoeff:"2.63", rfactor:"0.242", waters:"", solcontent:"53.23", ligands:"", metals:"", model:"False", uniprot:"Q98BZ3_RHILO", pubmed:"" } }}

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The mll5367 gene from Mesorhizobium loti encodes a choline/ethanolamine kinase (PF01633, COG0510, EC 2.7.1.32). The structure comprises two alpha+beta domains with a protein kinase-like fold that shows significant structural similarity to human cholin kinases (PDB id: 2IG7, 2I7Q). In bacteria, choline kinase is predicted to be involved in lipopolysaccharide (LPS) biosynthesis. The presence of phosphorylcholine on LPS has been shown to differentiate commensal from pathogenic bacteria [Ref], suggesting that this enzyme may play a broader role in immune avoidance.

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To do: look at ATP/choline binding sites

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{{ template.Protein{ leadContact:"", title:"Crystal structure of putative flavin reductase (YP_719437.1) from Haemophilus somnus 129PT at 1.06 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-08-21", targetid:"375038", pdbid:"2r0x", source:"Haemophilus somnus 129pt", relatedPDBs:[], refids:"HSOM_08NOV04_CONTIG98_REVISED_GENE995", molwt:"17197.55", residues:"157", isopoint:"5.92", sequence:"mvevsqfkdamaqlasavhivttsgetgqhgftasavcsvtdspptllvcinsnarayehfvknrvlmvn tltaeqsslsnifasplsqeerfsnaswttlttgspmlqdalinfdceiteikhvgthdilickivdih qsnaknalvyrnrvyhsv", method:"XRAY", numchains:"1", resolution:"1.06", rfree:"0.170", mattcoeff:"1.75", rfactor:"0.141", waters:"136", solcontent:"29.70", ligands:"ACT (ACETATE) x 5;SO4 (SULFATE) x 3;EDO (1,2-ETHANEDIOL) x 3", metals:"", model:"False", uniprot:"Q0I3S1_HAES1", pubmed:"" } }}

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See 2qck , same fold. Maybe check that the HHpred is also confirming this assignment.

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10760154

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{{ template.Protein{ leadContact:"", title:"",site:'JCSG', status:'Crystal Structure', date:"2009-11-19", targetid:"375169", pdbid:"", source:"Shewanella frigidimarina ncimb 400", relatedPDBs:[], refids:"YP_749235.1", molwt:"41058.55", residues:"372", isopoint:"5.25", sequence:"mtkaiqssvqvgelatgqaltvpiysfmgsensapsvyiqanvhgaevqgnaviyqlmtllegyqvlgdi tlaplanplginqksgeftlgrfdpitgvnwnreyfdhnvdiqnwyaehqhltnselfcayrsmlvetc qarlthsfgistghrlavnlqamahqadivldlhtgpksckhlycpeydidaarffsipytliipnsfg gamdeatfcpwwqlteyatsqgrefsvpvsaftlelasqeridladaledakgilaylshrgviaekvn pasmerfgcylkdykkfhapkaglieycasvgepltagkplvnilridlygseqayqaislpmdcvpil hfasasvlqgtelykvmtnvfplqps", method:"", numchains:"", resolution:"", rfree:"", mattcoeff:"", rfactor:"", waters:"", solcontent:"", ligands:"", metals:"", model:"False", uniprot:"", pubmed:"" } }}

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The protein YP_749235.1 is annotated as Succinylglutamate desuccinylase/aspartoacylase. YP_749235.1 belongs to PFAM PF04952 AstE_AspA which includes Succinylglutamate desuccinylase EC:3.1.-.- that catalyses the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway. The family also include aspartoacylase EC:3.5.1.15 which cleaves acylaspartate into a fatty acid and aspartate. Mutations in P45381 lead to Canavan disease disease [1]. This family is probably structurally related to PF00246 (Bateman A pers. obs.).

The protein has an unknown ligand (UNL) bound in the active site near Zn. The UNL resembles a derivative of Glutamate which could be related to Succinyl-Glutamate.

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{{ template.Protein{ leadContact:"", title:"Novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus. 2007",site:'JCSG', status:'In PDB', date:"2006-03-17", targetid:"367632", pdbid:"2gdt", source:"Sars coronavirus", relatedPDBs:["2hsx"], refids:"NP_828860.2", molwt:"12605.87", residues:"115", isopoint:"6.21", sequence:"hvqlslpvlqvrdvlvrgfgdsveealsearehlkngtcglvelekgvlpqleqpyvfikrsdalstnhg hkvvelvaemdgiqygrsgitlgvlvphvgetpiayrnvllrkng", method:"NMR", numchains:"1", resolution:"not", rfree:"", mattcoeff:"", rfactor:"", waters:"", solcontent:"", ligands:"", metals:"", model:"False", uniprot:"R1AB_CVHSA", pubmed:"17202208" } }}

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The gene NP_828860.2 from Sars coronavirus encodes a non-structural protein Nsp1 PF11501. The protein belongs to the class of alpha and beta (a+b) proteins and adopts a novel SARS Nsp1-like fold type SCOP16009. No significant protein functional motifs can be detected in the Nsp1 protein. Nsp1 is the "leader protein", it is translated from the most 5’ coding region of the SARS-CoV genome. The conservation of a viral protein indicates its importance in the virus life cycle. The Nsp1 sequence is highly conserved in SARS-CoV isolates sequenced from humans, civet cats and bats, implying that it is crucial to replication of the virus, survival in the host or spread in susceptible populations. The SARS-CoV Nsp1 is unique among coronaviruses and could contribute to the exceptional pathogenesis of SARS-CoV in humans. In cells, transfected with Nsp1 RNA, the decrease of host protein synthesis was observed. The inclusion of actinomycin D (to block new transcription) showed a much stronger inhibition of protein synthesis in the presence of Nsp1. This indicates that while translation of new transcripts was proceeding (in cells not treated with actinomycin D), translation from pre-existing transcripts was blocked by Nsp1. This suggests that Nsp1 increases RNA degradation. The exact mechanism of its action on RNA is not known. [Ref]

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17207625

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{{ template.Protein{ leadContact:"", title:"Crystal structure of conserved uncharacterized protein (ZP_00539648.1) from Exiguobacterium sp. 255-15 at 1.59 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-06-12", targetid:"375036", pdbid:"2q9k", source:"Exiguobacterium sp. 255-15", relatedPDBs:[], refids:"YP_001814466.1", molwt:"17064.62", residues:"150", isopoint:"5.29", sequence:"mankvehrlseqqmkaltdlplvflithdqskswpithaiswvyakdettirfaieadsllvktladhpv ftliffadqstysltctdvaawettarlplkvalyegqikevrdilfygaavsdrprvyktydeaaamq ldqqiqdilkg", method:"XRAY", numchains:"1", resolution:"1.59", rfree:"0.252", mattcoeff:"2.52", rfactor:"0.203", waters:"107", solcontent:"51.21", ligands:"UNL (UNKNOWN) x 1", metals:"", model:"False", uniprot:"Q41CU9_9BACI", pubmed:"" } }}

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The Exig_199 gene from Exiguobacterium sibiricum 255-15 has been found to encode for a pyridoxamine 5'-phosphate oxidase (PF01243, cl00381), an enzyme which catalyzes the reaction of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). The structure adopts a beta roll (2q9k-CATH). There is high structural similarity to several oxidoreductases like 1r1z [Ref] and PSI target 2ou5. Significant sequence homology to 2e83 (chain A), 3f7e (chain A) is detected by HHpred.

ToDo: Check if the ligand is plp,pnp or alike. Looks not like FMN (too small).

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14703520

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{{ template.Protein{ leadContact:"", title:"Crystal structure of hypothetical protein (tm0693) from Thermotoga maritima at 2.28 A resolution. ",site:'JCSG', status:'In PDB', date:"2006-02-10", targetid:"360368", pdbid:"2g42", source:"Thermotoga maritima", relatedPDBs:["2fzt"], refids:"TM0693", molwt:"9355.35", residues:"78", isopoint:"5.61", sequence:"mnideierkideaiekedyetllsllnkrkelmeglpkdklseilekdrkrleiiekrktalfqeinvir earsslqk", method:"XRAY", numchains:"2", resolution:"2.28", rfree:"0.251", mattcoeff:"2.18", rfactor:"0.203", waters:"72", solcontent:"43.23", ligands:"", metals:"CA (CALCIUM) x 1", model:"False", uniprot:"Q9WZF7_THEMA", pubmed:"" } }}

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The gene TM0693 from Thermotoga maritima encodes protein of unknown function DUF3214 PF11499. Another crystal structure of the same protein is available 2FZT. The protein belongs to the class of all alpha proteins and reveals methionine synthase domain-like fold type SCOP47643. However, the genome-wide BLAST sequence alignment search indicated close sequence identity (41%) of the protein to a S15 RNA-binding protein TCF52B from Thermosipho africanus. The small (30S) bacterial ribosomal subunit is composed of 16S rRNA and 21 distinct proteins. Ribosomal protein S15 binds primarily to 16S rRNA and is required for assembly of the small subunit and for intersubunit association, thus representing a key element in the assembly of a whole ribosome. The crystal structure of S15 from Thermus thermophilus in complex with rRNA demonstrates remarkable structural similarity to the TM0693 protein 1DK1 [Ref]. Thus, TM0693 might encode a putative S15 rRNA-binding protein.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of Putative Metal-dependent Phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis ATCC 15703 at 2.40 A resolution. ",site:'JCSG', status:'In PDB', date:"2008-07-31", targetid:"387987", pdbid:"3e0f", source:"Bifidobacterium adolescentis atcc 15703", relatedPDBs:[], refids:"YP_910028.1", molwt:"32528.45", residues:"300", isopoint:"5.19", sequence:"mshvsyaeppaqgwdihchtvfsdgtetprtlveqarklglhgvaiadhdttagwdeateaseeiglpll lgteitavdedvsvhmlafqydpsnehissmfantraarlrrtkrmverlsqdfpitwddvlaqvkege rttigrphiadalvaagvyetrsdafadavsakskyyiptpspstheviaavkgaggvvvaahagdpqr nrrllsdeqldamiadgldglevwhrgnppeqrerlltiaarhdllvtggsdwhgkgkpnglgenltdd dtvreilcrgvdligrvgsshaa", method:"XRAY", numchains:"1", resolution:"2.40", rfree:"0.207", mattcoeff:"2.50", rfactor:"0.149", waters:"103", solcontent:"50.75", ligands:"PO4 (PHOSPHATE) x 2;ACT (ACETATE) x 1", metals:"ZN (ZINC) x 1;FE (FE) x 2", model:"False", uniprot:"A1A2L3_BIFAA", pubmed:"" } }}

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The BAD_1165 gene from Bifidobacterium adolescentis atcc15703 encodes a putative metal-dependent phosphatase (PF02811, COG0613, EC 3.1.3.-) that adopts a 7-stranded beta/alpha barrel fold and shows strong structural similarity to other structures from this family solved by structural genomics (PDB id: 2ANU, 1M65). For more details on the biology and mechanism of this enzyme, see relevant publication [Ref].

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To do: check existence of trinuclear metal-binding site - could Fe sites be replaced by zinc?

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12661000

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{{ template.Protein{ leadContact:"", title:"Crystal structure of oleoyl thioesterase (putative) (NP_784467.1) from Lactobacillus plantarum at 2.00 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-02-16", targetid:"366924", pdbid:"2own", source:"Lactobacillus plantarum", relatedPDBs:[], refids:"NP_784467.1", molwt:"29917.32", residues:"261", isopoint:"5.13", sequence:"matlganaslyseqhrityyecdrtgratlttlidiavlasedqsdalglttemvqshgvgwvvtqyaid itrmprqdevvtiavrgsaynpyfayrefwirdadgqqlayitsiwvmmsqttrrivkilpelvapyqs evvkriprlprpisfeatdttitkpyhvrffdidpnrhvnnahyfdwlvdtlpatfllqhdlvhvdvry enevkygqtvtahanilpsevadqvttshlievddekccevtiqwrtlpepiq", method:"XRAY", numchains:"2", resolution:"2.00", rfree:"0.242", mattcoeff:"3.17", rfactor:"0.204", waters:"443", solcontent:"61.22", ligands:"SO4 (SULFATE) x 6;ACT (ACETATE) x 2;UNL (UNKNOWN) x 2;GOL (GLYCEROL) x 8", metals:"", model:"False", uniprot:"Q88YP1_LACPL", pubmed:"" } }}

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NP_784467.1 is a 261 residues long protein belonging to the Acyl Acyl-Carrier-Protein Thioesterase family (PF01643). It is composed of two 4-hydroxybenzoate thioesterase (4HBT) domains, from positions 10 to 120 and from 160 to 250. There are more than 500 sequences with this architecture present in all kingdoms. It crystallizes as a dimer, with an unknown ligand bound on equivalent positions on both A and B chains involving residues S45, W62, G87, A95 and R97, all part of the first 4HBT domain.

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SCOP classifies 2own inside the alpha+beta class, thioesterase/thiol ester dehydrase-isomerase superfamily, Acyl-ACP TE-like family. Top hits in HHpred and FFAS are 2ess, which corresponds to the equivalent enzyme in B. thetaiotamicron, and 1s5u, containing one single 4HBT domain. Dali and FATCAT corroborate the same hits with these values: 2ess (Z-scr=27.1; P-val=7e-12); 1s5u (Z-scr=18.6; P-val=5.5e-16).

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{{ template.Protein{ leadContact:"", title:"Crystal structure of uncharacterized protein SP_1565 (NP_346012.1) from Streptococcus pneumoniae TIGR4 at 2.00 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-06-07", targetid:"366227", pdbid:"2q7x", source:"Streptococcus pneumoniae tigr4", relatedPDBs:[], refids:"NP_346012.1", molwt:"36031.32", residues:"325", isopoint:"5.54", sequence:"mrkpkitvigggtgspvilkslrekdveiaaivtvaddggssgelrknmqqltppgdlrnvlvamsdmpk fyekvfqyrfsedagafaghplgnliiaglsemqgstynamqllskffhttgkiypssdhpltlhavfq dgtevageshivdhrgiidnvyvtnalnddtplasrrvvqtilesdmivlgpgslftsilpnivikeig ralletkaeiayvcnimtqrgetehftdsdhvevlhrhlgrpfidtvlvniekvpqeymnsnrfdeylv qvehdfvglckqvsrvissnflrlenggafhdgdlivdelmriiqvkk", method:"XRAY", numchains:"2", resolution:"2.00", rfree:"0.236", mattcoeff:"2.56", rfactor:"0.195", waters:"282", solcontent:"51.94", ligands:"PEG (DI(HYDROXYETHYL)ETHER) x 2", metals:"CL (CHLORIDE) x 1", model:"False", uniprot:"Y1565_STRPN", pubmed:"" } }}

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The SP_1565 gene from Streptococcus pneumoniae TIGR4 encodes for a protein of previously unknown function (PF01933, also known as UPF0052). The structure adopts a mainly helical fold and belongs to the class of LPPG:Fo 2-phospho-L-lactate transferases (CofD). There is considerable structural similarity to chain A of 3c3d [Ref], corroborated by a significant hit in HHpred. Therefore, evidence is given that this protein structure is a 2-phospho-(S)-lactate transferase. Other similar structures determined by the PSI include 2o2z, 2hzb, 2ppv, and 2p0y. See the TOPSAN PF01933 groups page for details.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of (tm1088a) from THERMOTOGA MARITIMA at 1.50 A resolution. ",site:'JCSG', status:'In PDB', date:"2006-02-14", targetid:"358957", pdbid:"2g1u", source:"Thermotoga maritima", relatedPDBs:[], refids:"TM1088A", molwt:"16032.54", residues:"143", isopoint:"5.12", sequence:"mskkqkskyivifgcgrlgslianlasssghsvvvvdkneyafhrlnsefsgftvvgdaaefetlkecgm ekadmvfaftnddstnffismnarymfnvenviarvydpekikifeengikticpavlmiekvkefiig seed", method:"XRAY", numchains:"1", resolution:"1.50", rfree:"0.175", mattcoeff:"2.44", rfactor:"0.153", waters:"110", solcontent:"49.14", ligands:"AMP (ADENOSINE) x 1;MPD ((4S)-2-METHYL-2,4-PENTANEDIOL) x 2", metals:"NA (SODIUM) x 1", model:"False", uniprot:"", pubmed:"" } }}

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The gene TM1088A from Thermotoga maritima encodes an N-terminal domain from TrkA protein (KTN) PF02254. The protein belongs to the class of alpha and beta (a+b) proteins and adopts a NAD(P)-binding Rossmann-domain fold type SCOP51734. KTN domain is a highly conserved cytoplasmic domain present ubiquitously in a variety of prokaryotic and eukaryotic K+ channels and transporters. KTN domain plays a central role in the regulation and coordination of K+ flux across cellular membranes. KTN domain forms tetramers in the solution in a ligand-dependent ( NAD+ and NADH) manner 1LSS [Ref]. These ligands are essential for maintenance of the tetrameric state of KTN in solution. Maintenance of cytoplasmic potassium levels is a vital homeostatic function, critical for cell growth and survival. Bacterial K+ transport systems are of medicinal interest, as they play central roles in the survival of pathogenic microbes in hostile host environments.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of Putative phosphatase (NP_812416.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.77 A resolution. ",site:'JCSG', status:'In PDB', date:"2009-12-04", targetid:"392960", pdbid:"3kya", source:"Bacteroides thetaiotaomicron vpi-5482", relatedPDBs:[], refids:"NP_812416.1", molwt:"55604.88", residues:"495", isopoint:"4.74", sequence:"kdddnvetgafdpskpvaisdftpkeggayqklliygenfgtdvskvkvkiggkdaivinvkstyvycfv psgafsgeieitvgegenavtttasttfsyekkmvvgtlcgyrnnrddqgwrdgpfdgpegvkccgfsd ngrlafdplnkdhlyicydghkaiqlidlknrmlssplnintiptnrirsiafnkkiegyadeaeymiv aidydgkgdespsvyiikrnadgtfddrsdiqliaaykqcngatihpingelyfnsyekgqvfrldlvd yfktiknggswdpivknnpntfkqlftiadpswefqifihptgkyayfgvinnhyfmrsdydeikkefi tpynfvggykqsgyrddvgtearmnnpcqgvfvknpdytgeeeydfyfvdrlnfcvrkvtpegivstya grgastsladgnqwgtddgdlrevarfrdvsglvyddvkemfyvhdqvghtirtismeqeenvagdeni pedestvesne", method:"XRAY", numchains:"1", resolution:"1.77", rfree:"0.198", mattcoeff:"2.59", rfactor:"0.175", waters:"427", solcontent:"52.56", ligands:"EDO (1,2-ETHANEDIOL) x 14;ACT (ACETATE) x 5", metals:"ZN (ZINC) x 9;CL (CHLORIDE) x 2", model:"False", uniprot:"Q8A204_BACTN", pubmed:"" } }}

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The BT_3504 gene from Bacteroides thetaiotaomicron encodes a protein of unknown function. The structure contains two domains. The N-terminal domain adopts an immunoglobulin-like fold and contains an IPT/TIG signature (PF01833, residues 19-100). IPT/TIG domains are found in cell surface receptors and intracellular transcription factors. However, genome context of BT_3504 (BT_3505, putative outer membrane protein, probably involved in nutrient binding) suggests cell surface localization. The C-terminal domain adopts a 6-bladed beta-propeller fold and shows strong homology (HHPred probability 99.6%, E-value 6.5E-14, P-value 6.4E-18 over residues 140-460) to the SGL family (SMP-30/Gluconolaconase/LRE-like region, PF08450), the NHL repeat (NCL-1, HT2A and LIN-41 repeat, PF01436) and MRJP (major royal jelly protein, PF03022).

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See also BT_3679 (PDB id 3HRP).

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12086676

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18252724

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{{ template.Protein{ leadContact:"", title:"Crystal structure of acetyltransferase (NP_689019.1) from Streptococcus agalactiae 2603 at 2.00 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-06-06", targetid:"370427", pdbid:"2q7b", source:"Streptococcus agalactiae 2603", relatedPDBs:[], refids:"NP_689019.1", molwt:"19550.45", residues:"162", isopoint:"7.75", sequence:"meikeyennpyhlaqlvdlinycqnieakldikmaeqddifqienyyqnrkgqfwialenekvvgsiall riddktavlkkfftypkyrgnpvrlgrklferfmlfaraskftrivldtpekekrshffyenqgfkqit rdeldvdyifpdrdsriyvklld", method:"XRAY", numchains:"1", resolution:"2.00", rfree:"0.223", mattcoeff:"2.65", rfactor:"0.185", waters:"92", solcontent:"53.60", ligands:"FLC (CITRATE) x 1", metals:"CL (CHLORIDE) x 1", model:"False", uniprot:"Q8DX25_STRA5", pubmed:"" } }}

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The Streptococcus agalactiae 2603 gene SAG2033 encodes for a GCN5-related N-acetyltransferase (GNAT), as given by for example 2q0y (structure comparison with TopMatch gives 19% sequence identity for 122 aligned residues with an rmsd of 2.4A).

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{{ template.Protein{ leadContact:"", title:"",site:'JCSG', status:'Crystal Structure', date:"2009-12-09", targetid:"400045", pdbid:"", source:"Mus musculus", relatedPDBs:[], refids:"NP_038806.2", molwt:"37041.85", residues:"323", isopoint:"6.67", sequence:"msskqhcvklndghlipalgfgtykpkevpksksleaaclaldvgyrhvdtayayqveeeigqaiqskik agvvkredlfvttklwctcfrpelvkpalekslkklqldyvdlyimhypvpmksgdndfpvneqgksll dtvdfcdtwerleeckdaglvksigvsnfnhrqlerilnkpglkykpvcnqvechlylnqrklldyces kdivlvaygalgtqrykewvdqnspvllndpvlcdvakknkrspalialryliqrgivplaqsfkenem renlqvfgfqlspedmktldglnknfrylpaeflvdhpeypfveey", method:"", numchains:"", resolution:"", rfree:"", mattcoeff:"", rfactor:"", waters:"", solcontent:"", ligands:"", metals:"", model:"False", uniprot:"", pubmed:"" } }}

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Structural basis for cofactor selectivity from the crystal structure of the mouse AKR1C13: NAD complex at 1.18Å resolution

This mouse protein is annotated as an AKR1C13 (aldo-keto reductase family 1, member C13) belonging to the aldo/keto reductase family PF00248 in Pfam. This is the first crystal structure of an AKR1C13 protein, although many crystal structures of other proteins have been solved from this protein family.

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The protein was subjected to reductive methylation after purification to facilitate crystallization and the modified residues are shown in sticks in the figure.

Endogenous NAD was modeled at the putative active site. This finding supports a biochemical study showing that AKR1C13 prefers NAD for function over NADP, as opposed to other related aldo-keto reductases (AKRs). The structure of this complex thus reveals the structural basis for this cofactor preference and selectivity.

In addition, endogenous MPD (2,4-methylpentanediol) was found in the structure near the NAD. Interestingly, some of the other related crystal structures have bound MPD, but in those cases, the MPD is from the crystallization condition.

It is likely that this bound MPD may mimic natural substrate since the expected ligands for AKR1C13 are non-steroidal alcohols (like s-tetralol, geraniol and farnesol), which are smaller than the steroidal alcohols that are the substrates for other AKRs.

A comparison of the residues involved in interactions with NAD and MPD and critical residues in the other AKRs will be provided later along with some analysis how these different family members may have evolved. A more thorough analysis is in progress.

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References:

1)Characterization of rat and mouse NAD+-dependent 3alpha/17beta/20alpha-hydroxysteroid dehydrogenases and identification of substrate specificity determinants by site-directed mutagenesis. Endo S, Sanai M, Horie K, Matsunaga T, Ishikura S, Tajima K, El-Kabbani O, Hara A. Arch Biochem Biophys. 2007 Nov 1;467(1):76-86. Epub 2007 Aug 24.PMID: 17888864

2)Cloning and characterization of two novel aldo-keto reductases (AKR1C12 and AKR1C13) from mouse stomach. Ikeda S, Okuda-Ashitaka E, Masu Y, Suzuki T, Watanabe K, Nakao M, Shingu K, Ito S. FEBS Lett. 1999 Oct 15;459(3):433-7.PMID: 10526179

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{{ template.Protein{ leadContact:"", title:"Crystal structure of pyridoxamine 5'-phosphate oxidase-related FMN-binding (YP_508196.1) from Jannaschia sp. CCS1 at 1.60 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-02-09", targetid:"370379", pdbid:"2ou5", source:"Jannaschia sp. ccs1", relatedPDBs:[], refids:"YP_508196.1", molwt:"19178.90", residues:"174", isopoint:"9.35", sequence:"msdtvltglldtvwqqfgrgtkdrhhparhptlatigtdgpdlrtlvlraashaeatlefhtdaaspkva hirrdarvaihiwipkaslqvrakaiakilpgdpnlfaqlpeaarmnyqgpvpgtplpaepdatpnrft rlichlseidvlhlttphqravytapdwrgiwvsp", method:"XRAY", numchains:"2", resolution:"1.60", rfree:"0.221", mattcoeff:"2.27", rfactor:"0.178", waters:"413", solcontent:"45.80", ligands:"SO4 (SULFATE) x 1;FMN (FLAVIN) x 2;GOL (GLYCEROL) x 4", metals:"", model:"False", uniprot:"Q28VU1_JANSC", pubmed:"" } }}

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YP_508196.1 is a 174 residues long polypeptide containing a Pyridoxamine 5'-phosphate Oxidase like domain (PNPOx) between residues 30 to 100. This class of enzymes (PF01243) catalyzes the conversion of pyridoxamine-5-phosphate to pyridoxal-5-phosphate using flavin mono-nucleotide (FMN) as cofactor. This dimeric crystal structure, 2os5, presents 2 FMN molecules, each interacting with three regions of the protein around residues: R44-T45-V47; H61-T62-K68; Q90-R92. Based on the genome context where the gene codifying this protein is located, a predicted functional partner is YP_508198.

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SCOP classifies 2os5 as an all beta structure in the superfamily FMN-binding split barrel, family PNPOx-like. Structural comparison searches provide the PNPOx-like structures 1ci0, 1t9m and 1dnl as the most similar.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of N-formylglutamate amidohydrolase (YP_297560.1) from Ralstonia eutropha JMP134 at 2.00 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-06-07", targetid:"374214", pdbid:"2q7s", source:"Ralstonia eutropha jmp134", relatedPDBs:[], refids:"YP_297560.1", molwt:"32549.22", residues:"289", isopoint:"5.84", sequence:"mnqamdtkqiapftlalpegealplvcdsphsgtfypadfgavvaperlrggedthvdalweavprvggt llaatfprvyidpnrmlddidpaqlegpwptplapgektrlgygliwsnvdaatpiydrkltvaevqrr inryyrpyhaalteavegayqrfgavwhlnlhsmpnnayerlkiqsprpladfvlgdrdgttcepglvd lverelrekgytvarndpykgvqliaqigrpaerrnslqieirrplymeegtrernegfatlqrdltll tlriaeyvrrgv", method:"XRAY", numchains:"2", resolution:"2.00", rfree:"0.246", mattcoeff:"2.42", rfactor:"0.199", waters:"297", solcontent:"49.14", ligands:"", metals:"ZN (ZINC) x 2", model:"False", uniprot:"Q46VW8_RALEJ", pubmed:"" } }}

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The Reut_A3358 gene from Ralstonia eutropha jmp134 (PF05013, cl01522) encodes for a N-formylglutamate amidohydrolase which catalyzes the terminal reaction in the five-step pathway for histidine utilization, providing the organism with a source of nitrogen and carbon. The protein adopts a three layer alpha/beta/alpha sandwich and the functional biomolecule is a single-domain monomer (2q7s-CATH, 2q7s-SCOP). Another structural highly similar protein, 2odf, was determined by the PSI.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of hypothetical protein (NP_252042.1) from Pseudomonas aeruginosa at 1.48 A resolution. ",site:'JCSG', status:'In PDB', date:"2006-01-27", targetid:"369551", pdbid:"2fup", source:"Pseudomonas aeruginosa", relatedPDBs:[], refids:"NP_252042.1", molwt:"17254.42", residues:"156", isopoint:"5.55", sequence:"mpdsptlldlfaedighanqllqlvdeefqalerrelpvlqqllgakqplmqqlerngraraeilreagv sldreglaryareradgaellargdelgellercqqanlrngriiranqastgsllnilrgqdapslyd srggtasssrqrplska", method:"XRAY", numchains:"1", resolution:"1.48", rfree:"0.218", mattcoeff:"2.25", rfactor:"0.188", waters:"110", solcontent:"45.32", ligands:"MPD ((4S)-2-METHYL-2,4-PENTANEDIOL) x 1", metals:"", model:"False", uniprot:"", pubmed:"" } }}

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The gene NP_252042.1 from Pseudomonas aeruginosa encodes a FlgN-like protein PF05130. The protein belongs to the class of all alpha proteins and adopts a STAT-like fold type SCOP47654. FlgN-like proteins are structurally related to type III secretion chaperones [Ref]. The function of FlgN is to facilitate the initiation of flagella filament assembly, a role that may be critical in attaining the much higher concentration of surface flagellin required for swarming. It has been shown in vitro that FlgN specifically binds to flagellar proteins [Ref]. The flagellar axial proteins destinedforpolymerization into the cell surface structure are exported through the25–30 A ̊flagellumcentral channel as partially unfolded monomers. Thus, most probably FlgN functions as export chaperone [Ref].

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10320579

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9302021

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{{ template.Protein{ leadContact:"", title:"Crystal structure of Tellurite resistance protein of COG3793 (ZP_00109916.1) from Nostoc punctiforme PCC 73102 at 1.85 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-02-09", targetid:"373118", pdbid:"2ou3", source:"Nostoc punctiforme pcc 73102", relatedPDBs:[], refids:"NPUN_22DEC03_CONTIG1_REVISED_GENENPF6341", molwt:"18254.90", residues:"160", isopoint:"4.81", sequence:"msdikklgsswiinwffgfnqiptnedssiymksvltcakadgvispeekdwalgfcaswgvadwviedl ktyeadealeeviarspqvsmaqrdillsaiwvsaadgelhekekakirkmatilgikeeivdqleqly yyeaalrqkrlnllypqkspy", method:"XRAY", numchains:"2", resolution:"1.85", rfree:"0.213", mattcoeff:"2.22", rfactor:"0.161", waters:"395", solcontent:"44.66", ligands:"I3A (1H-INDOLE-3-CARBALDEHYDE) x 2;EDO (1,2-ETHANEDIOL) x 2", metals:"ZN (ZINC) x 5;CL (CHLORIDE) x 1", model:"False", uniprot:"", pubmed:"" } }}

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YP_001869556 is a hypothetical protein that belongs to the Tellurite resistance protein B-like superfamily (PF05099), with more than 650 bacterial representatives with the same domain architecture. Its HMM profile shows a highly conserved sequence pattern: D37-E44--D110-E117. The structure solved here, 2ou3, shows a Zn ion chelated by the equivalent residues: D42-E49--D107-E114.

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SCOP classifies 2ou3 as belonging to the all-alpha class, TerB-like superfamily, COG3793-like family. HHpred and FFAS provide hits with the TerB-like proteins 2jxu (Pval=2.1e-23; score=-36.8) and 2h5n (Pval=1.6e-9; score=-15.2). Structural comparison servers consistently selected 2h5n as top hit: SSM sse=63%; Dali Z-scr=7.6; FATCAT P-val=6.5e-6.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of uncharacterized protein (YP_323524.1) from Anabaena variabilis ATCC 29413 at 2.11 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-05-25", targetid:"367679", pdbid:"2q22", source:"Anabaena variabilis atcc 29413", relatedPDBs:[], refids:"YP_323524.1", molwt:"15225.82", residues:"138", isopoint:"5.90", sequence:"msmpnhpnlttadakkilnkfncldiapilkpsekesvrralilitklsdyqilgicadtadegllamkt yshalgyevpidlpvvegpvyiklngknglcyldsyaghhrgvlvscqsyyegginemyghlpldlfv", method:"XRAY", numchains:"3", resolution:"2.11", rfree:"0.222", mattcoeff:"2.84", rfactor:"0.191", waters:"191", solcontent:"56.75", ligands:"ACT (ACETATE) x 4;PG4 (TETRAETHYLENE) x 2;EDO (1,2-ETHANEDIOL) x 2", metals:"CL (CHLORIDE) x 3", model:"False", uniprot:"Q3M8Q7_ANAVT", pubmed:"" } }}

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This protein structure from Anabaena variabilis atcc 29413 is the product of the Ava_3019 gene and belongs to a family with unknown function. The structure adopts an alpha+beta fold. Its PFAM idenitification code is PF08854 (also known as DUF1824). At the time of editing, some structural similarity was found to the N-terminal domain of chain A of 1y4u (a Hsp90 chaperone from E. coli). We refer the reader to PF08854 group on this server.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of Phosphohydrolase (BT4208) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-05-23", targetid:"356887", pdbid:"2q14", source:"Bacteroides thetaiotaomicron vpi-5482", relatedPDBs:[], refids:"BT4208", molwt:"46944.39", residues:"409", isopoint:"5.88", sequence:"mpyerkiindpvfgfinipkgllydivrhpllqrltrikqvglssvvypgaqhtrfqhslgafylmseai tqltskgnfifdseaeavqaaillhdighgpfshvledtivqgvsheeislmlmermnkemngqlslai qifkdeypkrflhqlvsgqldmdrldylrrdsfytgvtegnigsariikmldvaddrlvieskgiysie nfltarrlmywqvylhktsvayermlistllrakelasqgvelfaspalhfflyndinhtefhnnpdcl enfiqlddndiwtalkvwsnhpdkvlstlslgminrnifkvensaepigedrikeltlqisqqlgitls eanyfvstpsieknmydpaddsidiiykdgtikniaeasdmlnisllskkvkkyylcyqrlhr", method:"XRAY", numchains:"8", resolution:"2.20", rfree:"0.252", mattcoeff:"2.90", rfactor:"0.207", waters:"1624", solcontent:"57.63", ligands:"ADP (ADENOSINE-5'-DIPHOSPHATE) x 8;EDO (1,2-ETHANEDIOL) x 6;GOL (GLYCEROL) x 3", metals:"CL (CHLORIDE) x 3", model:"False", uniprot:"Q8A013_BACTN", pubmed:"" } }}

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The BT_4208 gene from Bacteroides thetaiotaomicron VPI-5482 encodes for a metal dependent phosphohydrolase (PF01966, cl00076) found in bacteria, archaea and eukaryotes. The protein adopts a mainly alpha helical fold. The functional biomolecule is a tetramer, according to both the author and PISA software. The octamer asymmetric unit holds two biomolecules. According to CATH, each chain is composed of two domains (2q14-CATH). Protein structures with very high structural similarity and sequence identity >30% include the PSI determined 2ogi and 2hek [Ref].

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17565173

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{{ template.Protein{ leadContact:"", title:"Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 A resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases. 2007",site:'JCSG', status:'In PDB', date:"2005-11-22", targetid:"367330", pdbid:"2f46", source:"Neisseria meningitidis z2491", relatedPDBs:[], refids:"7380613", molwt:"17682.20", residues:"155", isopoint:"6.91", sequence:"mpsekqpqskgnkmailkldehlyispqltkadaeqiaqlgiktiicnrpdreeesqpdfaqikqwleqa gvtgfhhqpvtardiqkhdvetfrqligqaeypvlaycrtgtrcsllwgfrraaegmpvdeiirraqaa gvnlenfrerldnarv", method:"XRAY", numchains:"2", resolution:"1.41", rfree:"0.228", mattcoeff:"2.01", rfactor:"0.2", waters:"411", solcontent:"38.69", ligands:"UNL (UNKNOWN) x 1", metals:"CL (CHLORIDE) x 2", model:"False", uniprot:"", pubmed:"17636569" } }}

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The gene 7380613 from Neisseria meningitidis z2491 encodes a protein tyrosine phosphatase (PTP). The enzyme belongs to the class of alpha and beta (a+b) proteins and adopts a phosphotyrosine protein phosphatases II fold type SCOP52798. The structure of close homologue of the enzyme from Arabidopsis thaliana has been determined 1XRI. The phosphatase activity of the enzyme was confirmed in vitro [Ref]. The overall fold of this phosphatase resembles that of eukaryotic-like phosphatases, PTP1B in particular 1PTY. N. meningitidis is an important human pathogen responsible for causing meningitis and septicaemia, which are debilitating diseases that kill thousands of people every year. Thus, this phosphatase might be a very promising target for therapeutic intervention.

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17636569

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{{ template.Protein{ leadContact:"", title:"Crystal structure of 16S rRNA processing protein from Pseudomonas aeruginosa at 2.46 A resolution. ",site:'JCSG', status:'In PDB', date:"2005-11-14", targetid:"357814", pdbid:"2f1l", source:"Pseudomonas aeruginosa", relatedPDBs:[], refids:"NP_252433.1", molwt:"19788.51", residues:"175", isopoint:"4.86", sequence:"mptpaddlvvigkivsvygirgevkvysftdpldnlldyrrwtlrrdgeirqaelvrgrlhgkvlaaklk glddreeartftgyeiciprselpsleegeyywhqleglkvidqgrqllgvidhlletgandvmvvkpc agslddrerllpytgqcvlsidlaagemrvdwdadf", method:"XRAY", numchains:"1", resolution:"2.46", rfree:"0.237", mattcoeff:"3.41", rfactor:"0.175", waters:"44", solcontent:"63.68", ligands:"UNL (UNKNOWN) x 2;GOL (GLYCEROL) x 3", metals:"", model:"False", uniprot:"", pubmed:"" } }}

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The gene NP_252433.1 from Pseudomonas aeruginosa encodes a putative 16S rRNA processing protein RimM (N-terminal domain). The protein adopts a reductase/isomerase/elongation factor common domain fold type SCOP50412. In accord with the fold type, the second functional (C-terminal) domain is hotosynthetic reaction center (RC) complex, subunit H (PRCH) PF05239 is detected. RC catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce ATP by ATP synthase. PRCH is positioned mainly in the cytoplasm with one transmembrane alpha helix. It provides proton transfer pathway (water channels) connecting the terminal quinone electron acceptor of RC, to the aqueous phase. Within the context of 16S rRNA processing protein, this domain might be involved in hydrophilic substrate (RNA) binding. Structures of the protein homologues fro other organisms have been determined: 3H9N, Haemophilus influenzae; 2DOG, Thermus thermophilus HB8.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of uncharacterized protein (YP_001166107.1) from Novosphingobium aromaticivorans DSM 12444 at 1.16 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-10-01", targetid:"378075", pdbid:"2rfr", source:"Novosphingobium aromaticivorans dsm 12444", relatedPDBs:[], refids:"SARO_25NOV03_CONTIG22_REVISED_GENE168", molwt:"16712.87", residues:"154", isopoint:"6.42", sequence:"mddltnlaarlrlledreeireliarygpladsgdaealselwvedgeyavvgfatakgraaiaalidgq thralmadgcahflgpatvtvegdtatarchsvvfrcvsgtfgshrvsanrwtfrrtpagwravrrena lldgsaaarallqfr", method:"XRAY", numchains:"1", resolution:"1.16", rfree:"0.172", mattcoeff:"2.56", rfactor:"0.141", waters:"272", solcontent:"51.94", ligands:"", metals:"", model:"False", uniprot:"A4XF70_NOVAD", pubmed:"" } }}

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The Saro_3722 gene from Novosphingobium aromaticivorans dsm 12444 encodes a protein of unknown function that adopts a cystatin-like fold. There are no PfamA or PfamB matches for this protein although HHPred give strong hits with families from the NTF2 clan (PF00866, PF08332, PF02982, PF02156 and PF07858). The structure shows significant similarity to numerous other members of the same clan determined by structural genomics (PDB id: 2RGQ, 3CU3, 3EF8, 3EJV, 3HX8, 3B8L, 3CNX, 3GZR).

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{{ template.Protein{ leadContact:"", title:"Solution structure of Asl1650, an acyl carrier protein from Anabaena sp. PCC 7120 with a variant phosphopantetheinylation-site sequence. 2006",site:'JCSG', status:'In PDB', date:"2005-07-25", targetid:"354432", pdbid:"2afd", source:"Nostoc sp. pcc 7120", relatedPDBs:["2afe"], refids:"17135470", molwt:"9830.70", residues:"85", isopoint:"4.17", sequence:"mktiqpcsvediqswlidqfaqqldvdpddidmeesfdnydlnsskalillgrlekwlgkelnpvlifny ptiaqlakrlgelyl", method:"NMR", numchains:"1", resolution:"not", rfree:"", mattcoeff:"", rfactor:"", waters:"", solcontent:"", ligands:"", metals:"", model:"False", uniprot:"Q8YWG3_ANASP", pubmed:"16597827" } }}

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The gene 17135470 from Anabaena sp. encodes an acyl carrier protein, a member of phosphopantetheine binding domain proteins PF00550. The protein belongs to the class of all alpha proteins and reveals an acyl carrier protein-like fold type SCOP47335. The protein adopts a twisted antiparallel four-helix bundle fold, with a variant phosphopantetheine-attachment motif positioned at the start of the second helix. Structure comparisons with proteins from other organisms suggests a likely physiological function as a discrete peptidyl carrier protein [Ref]. The crystal structure of the protein homologue from Thermotoga maritima is available 1VKU.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of a putative nucleotidyltransferase (NP_343093.1) from Sulfolobus solfataricus at 1.40 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-09-28", targetid:"376473", pdbid:"2rff", source:"Sulfolobus solfataricus", relatedPDBs:[], refids:"NP_343093.1", molwt:"12822.29", residues:"110", isopoint:"6.33", sequence:"mgkgksaiesqirmlklakeiveevassfpnleevyifgsrargdyldtsdidilfvfkgikemnvfdrm ymvsrfirgnvdyivldegekdrvkdkvlfwkrekgfvll", method:"XRAY", numchains:"1", resolution:"1.40", rfree:"0.187", mattcoeff:"1.85", rfactor:"0.145", waters:"107", solcontent:"33.65", ligands:"EDO (1,2-ETHANEDIOL) x 2", metals:"", model:"False", uniprot:"Q97XP0_SULSO", pubmed:"" } }}

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The SSO1673 gene from Sulfolobus solfataricus encodes a putative nucleotidyltransferase (PF01909, COG1708, EC 2.7.7.-) that adopts a nucleotidyltransferase fold and shows significant structural similarity with antibiotic nucleotidyltransferases (PDB id: 1KNY, 3JZ0) and other nucleotidyltransferases determined by structural genomics (PDB id: 1YLQ).

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To do: carry out closer comparison of antibiotic nucleotidyltransferases with SSO1673

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{{ template.Protein{ leadContact:"", title:"Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1''-phosphate dephosphorylation by a conserved domain of nsP3. 2005",site:'JCSG', status:'In PDB', date:"2005-07-18", targetid:"367631", pdbid:"2acf", source:"Sars coronavirus tor2 isolate", relatedPDBs:[], refids:"29837497", molwt:"18711.65", residues:"175", isopoint:"8.10", sequence:"pvnqftgylkltdnvaikcvdivkeaqsanpmvivnaanihlkhgggvagalnkatngamqkesddyikl ngpltvggscllsghnlakkclhvvgpnlnagediqllkaayenfnsqdillapllsagifgakplqsl qvcvqtvrtqvyiavndkalyeqvvmdyldnlkprv", method:"XRAY", numchains:"4", resolution:"1.40", rfree:"0.18916", mattcoeff:"2.60", rfactor:"0.16414", waters:"950", solcontent:"51.00", ligands:"GOL (GLYCEROL) x 12", metals:"", model:"False", uniprot:"", pubmed:"16271890" } }}

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The gene 29837497 from Sars coronavirus encodes a conserved domain of nonstructural protein 3 (nsP3), a member of a macro family PF01661 SCOP52948. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. The SARS nsP3 domain readily removes the 1'' phosphate group from Appr-1''-p in in vitro assays, confirming its phosphatase activity [Ref].

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16271890

Summary

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{{ template.Protein{ leadContact:"", title:"Crystal structure of (np_841403.1) from NITROSOMONAS EUROPAEA at 1.90 A resolution. ",site:'JCSG', status:'In PDB', date:"2005-07-02", targetid:"358727", pdbid:"2a6c", source:"Nitrosomonas europaea", relatedPDBs:[], refids:"NP_841403.1", molwt:"7938.99", residues:"71", isopoint:"8.16", sequence:"mkmrsqllivlqehlrnsgltqfkaaellgvtqprvsdlmrgkidlfsleslidmitsiglkveinikda a", method:"XRAY", numchains:"2", resolution:"1.90", rfree:"0.241", mattcoeff:"2.30", rfactor:"0.182", waters:"72", solcontent:"46.01", ligands:"EDO (1,2-ETHANEDIOL) x 1;CIT (CITRIC) x 1;GOL (GLYCEROL) x 2", metals:"", model:"False", uniprot:"Q82UW4_NITEU", pubmed:"" } }}

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The gene NP_841403.1 from Nitrosomonas europaea encodes a putative XRE-family transcription regulator (based on 52% sequence identity with XRE regulator from Burkholderia ambifaria MEX-5), a member of DNA-binding domain Helix-Turn-Helix (HTH) superfamily PF01381. The protein belongs to the class of all alpha proteins and adopts a lambda repressor-like DNA-binding domain fold type SCOP47412. Prokaryotic XRE-family DNA binding proteins are the xenobiotic response element family of transcriptional regulators. The structures of the protein homologues from other organisms have been solved: 3F6W, Pseudomonas syringae; 2O38, Rhodopseudomonas palustris; 1Y7Y, Aeromonas hydrophila.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of hypothetical protein MJ_1460 (1592102) from Methanococcus jannaschii at 2.30 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-02-05", targetid:"373077", pdbid:"2osd", source:"Methanococcus jannaschii", relatedPDBs:["2oso"], refids:"1592102", molwt:"18887.10", residues:"162", isopoint:"4.81", sequence:"mafmekifpdileairneeiikeskkipmpyfglfalvifdkvkelgsetslyeigeefgkmlspkniee lkkifklmnfgdleidenkillknppykiklsnppyqwvskeepihdfiagilagcleeifyyyfvvne vecvsqgkdkcvfevkevdelnk", method:"XRAY", numchains:"1", resolution:"2.30", rfree:"0.242", mattcoeff:"2.41", rfactor:"0.219", waters:"30", solcontent:"48.95", ligands:"EDO (1,2-ETHANEDIOL) x 3", metals:"CA (CALCIUM) x 2;CL (CHLORIDE) x 1;ZN (ZINC) x 1", model:"False", uniprot:"Y1460_METJA", pubmed:"" } }}

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MJ_1460 is a 162 residues hypothetical protein containing a ~60 residues long V4R (vinyl-4-reductase) domain at its C-terminus (PF02830). So far, 185 proteins, all from prokaryotes, share the same domain architecture. Its HMM profile shows high conservation of a sequence motif C/H-E-C-C. The equivalent residues in 2osd (H116-E139-C142-C150) chelate a Zn ion in the crystal structure.

SCOP classifies 2osd as belonging to the alpha-beta class, superfamily of "ligand binding in the NO signaling and Golgi transport". In agreement, a subunit of the ER-Golgi protein traffiking complex 2j3w is a relevant hit coming from HHpred (P-val=1.3e-6), FATCAT (P-val=1.15e-4), Dali (Z-scr=10.5) and FFAS (score -10.3); and 2o09 , a Heme-NO binding domain, is selected by both SSM (75% SSE) and FFAS (score -11.4). A different H-NOX structure, 1u55, is detected by fastSCOP (e-val=2e-8) and FATCAT (P-val=2.25e-5).

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User:DELAUNAY

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{{ template.Protein{ leadContact:"", title:"Crystal structure of General Stress Protein COG3871 (YP_263493.1) from Psychrobacter arcticus 273-4 at 2.50 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-09-25", targetid:"380202", pdbid:"2re7", source:"Psychrobacter arcticum 273-4", relatedPDBs:[], refids:"YP_263493.1", molwt:"14872.01", residues:"133", isopoint:"4.95", sequence:"msnqkhidkiqavikdvkfamistsnkkgdihawpmttsevnldnkeiwfigdktsdvvkdiqddarigl tyatqdeknyvsisgdaelptdkakldelwspvysaffangkedaniqlikvvphgvecwlsg", method:"XRAY", numchains:"1", resolution:"2.50", rfree:"0.226", mattcoeff:"3.39", rfactor:"0.191", waters:"24", solcontent:"63.71", ligands:"SO4 (SULFATE) x 2", metals:"", model:"False", uniprot:"Q4FV99_PSYAR", pubmed:"" } }}

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The Psyc_0186 gene from Psychrobacter arcticum 273-4 encodes a pyridoxamine 5'-phosphate oxidase found in all domains of life (PF01243, EC 1.4.3.5). The structure belongs to the FMN-binding split barrel superfamily and shows strong structural similarity (rmsd <2Å, >100 aligned residues) to other structural genomics structures (PDB ids: 2FHQ, 2I02, 3EC6, 2ASF, 2HQ7, 2HTI, 2HTD, 2QEA) from the same family.

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To do: check dimerization mode, FMN and substrate binding site conservation, connection to stress/salvage pathways.

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{{ template.Protein{ leadContact:"", title:"NMR Structure of the Conserved Hypothetical Protein Tm0487 from Thermotoga Maritima: Implications for 216 Homologous Duf59 Proteins. 2005",site:'JCSG', status:'In PDB', date:"2004-02-03", targetid:"282360", pdbid:"1uwd", source:"Thermotoga maritima", relatedPDBs:["1wcj"], refids:"TM0487", molwt:"11637.98", residues:"104", isopoint:"4.39", sequence:"mpmskkvtkedvlnalknvidfelgldvvslglvydiqiddqnnvkvlmtmttpmcplagmilsdaeeai kkiegvnnveveltfdppwtpermspelrekfgv", method:"NMR", numchains:"1", resolution:"not", rfree:"", mattcoeff:"", rfactor:"", waters:"", solcontent:"", ligands:"", metals:"", model:"False", uniprot:"Q9WYV7", pubmed:"16199668" } }}

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The gene TM0487 from Thermotoga maritima encodes a protein of unknown function DUF59 PF01883. The BLAST alignment indicates 53% sequence identity to a putative dTDP-4-keto-l-rhamnose reductase EC:1.1.1.133 from Pyrococcus abyssi GE5 COG1091. The structure comparison with the enzyme homologues from Thermus Thermophilus HB8, 2CU6 3CQ1 also suggests that given protein is most probably dTDP-4-keto-l-rhamnose reductase. The enzyme catalyzes the following reaction: dTDP-6-deoxy-L-mannose + NADP(+) <=> dTDP-4-dehydro-6-deoxy-L-mannose + NADPH. The enzyme participates in 3 metabolic pathways: nucleotide sugars metabolism, streptomycin biosynthesis, and polyketide sugar unit biosynthesis.

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{{ template.Protein{ leadContact:"", title:"Crystal structure of GCN5-related N-acetyltransferase (YP_295895.1) from Ralstonia eutropha JMP134 at 1.80 A resolution. ",site:'JCSG', status:'In PDB', date:"2007-05-22", targetid:"371710", pdbid:"2q0y", source:"Ralstonia eutropha jmp134", relatedPDBs:[], refids:"YP_295895.1", molwt:"17063.72", residues:"152", isopoint:"5.33", sequence:"mecrplciddlelvcrhreamfreagrdaltlaamqdpfrdwllprladgsyfgwvmeeggaplagiglm viewpphpshplqdkrgyilnlyvdpshrergigqalmnraeaefaergiafavlhatemgqplyarmg wspttemskpiag", method:"XRAY", numchains:"1", resolution:"1.80", rfree:"0.165", mattcoeff:"3.53", rfactor:"0.143", waters:"206", solcontent:"65.15", ligands:"UNL (UNKNOWN) x 1;EDO (1,2-ETHANEDIOL) x 1;FMT (FORMIC) x 4", metals:"ZN (ZINC) x 1;MG (MAGNESIUM) x 2", model:"False", uniprot:"Q470Y2_RALEJ", pubmed:"" } }}

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The Ralstonia eutropha jmp134 gene Reut_A1686 encodes for a GCN5-related N-acetyltransferase (GNAT, PF00583, cl00443, EC 2.3.1.-), an enzyme that catalizes the transfer of an acetyl group to lysine in histones. The biological functional unit is a dimer. The protein structure belongs to the alpha/beta class and adopts a three3 layer alpha/beta/alpha sandwich (2q0y-CATH). Similar structures have been determined by PSI such as 3dsb, 3f0a, 1tiq (also see [Ref]).An introduction to the structural role of histone acetyltransferases (HATs) is given by [Ref] which can be retrieved freely downloadedhere freely.

ToDo: Determine the ligand. Maybe by structural superposition.

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16210326

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{{ template.Protein{ leadContact:"", title:"Solution structures of the putative anti-sigma-factor antagonist TM1442 from Thermotoga maritima in the free and phosphorylated states. 2006",site:'JCSG', status:'In PDB', date:"2004-02-10", targetid:"283301", pdbid:"1t6r", source:"Thermotoga maritima", relatedPDBs:["1sbo"], refids:"TM1442", molwt:"12299.53", residues:"110", isopoint:"5.81", sequence:"mnnlkldiveqddkaivrvqgdidaynsselkeqlrnfisttskkkivldlssvsymdsaglgtlvvilk dakingkefilsslkesisrilklthldkifkitdtveea", method:"NMR", numchains:"1", resolution:"not", rfree:"", mattcoeff:"", rfactor:"", waters:"", solcontent:"", ligands:"", metals:"", model:"False", uniprot:"Y1442_THEMA", pubmed:"16826544" } }}

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The gene TM1442 from Thermotoga maritima encodes an anti-sigma factor antagonist domain of anti-anti-sigma factors (the STAS domain) PF01740 COG1366. The crystal structure of the same protein is available 1SBO. Anti-anti-sigma factors play an important role in the regulation of several sigma factors and their corresponding anti-sigma factors. Upon dephosphorylation they bind the anti-sigma factor and induce the release of the sigma factor from the anti-sigma factor. In a feedback mechanism the anti-anti-sigma factor can be inactivated via phosphorylation by the anti-sigma factor. Well studied examples from Bacillus subtilis are SpoIIAA (regulating sigmaF and sigmaC which play an important role in sporulation) and RsbV (regulating sigmaB involved in the general stress response) [Ref]. The STAS domain is also found in the C-terminal region of sulphate transporters and stressosomes.

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