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< | ==Crystal structure of putative metal-dependent hydrolase APC36150== | ||
<StructureSection load='3gor' size='340' side='right'caption='[[3gor]], [[Resolution|resolution]] 2.51Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3gor]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3e4x 3e4x]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GOR FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gor OCA], [https://pdbe.org/3gor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gor RCSB], [https://www.ebi.ac.uk/pdbsum/3gor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gor ProSAT]</span></td></tr> | |||
</table> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/go/3gor_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3gor ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The crystal structure of the dinB gene product from Geobacillus stearothermophilus (GsDinB) is reported at 2.5 A resolution. The dinB gene is one of the DNA-damage-induced genes and the corresponding protein, DinB, is the founding member of a Pfam family with no known function. The protein contains a four-helix up-down-down-up bundle that has previously been described in the literature in three disparate proteins: the enzyme MDMPI (mycothiol-dependent maleylpyruvate isomerase), YfiT and TTHA0303, a member of a small DUF (domain of unknown function). However, a search of the DALI structural database revealed similarities to a further 11 new unpublished structures contributed by structural genomics centers. The sequences of these proteins are quite divergent and represent several Pfam families, yet their structures are quite similar and most (but not all) seem to have the ability to coordinate a metal ion using a conserved histidine-triad motif. The structural similarities of these diverse proteins suggest that a new Pfam clan encompassing the families that share this fold should be created. The proteins that share this fold exhibit four different quaternary structures: monomeric and three different dimeric forms. | |||
The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily.,Cooper DR, Grelewska K, Kim CY, Joachimiak A, Derewenda ZS Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Mar 1;66(Pt, 3):219-24. Epub 2010 Feb 23. PMID:20208147<ref>PMID:20208147</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3gor" style="background-color:#fffaf0;"></div> | |||
[[Category: | == References == | ||
[[Category: Cooper, D R | <references/> | ||
[[Category: Derewenda, Z S | __TOC__ | ||
[[Category: Grelewska, K | </StructureSection> | ||
[[Category: ISFI, Integrated Center for Structure and Function Innovation | [[Category: Atcc 12980]] | ||
[[Category: Large Structures]] | |||
[[Category: Cooper, D R]] | |||
[[Category: Derewenda, Z S]] | |||
[[Category: Grelewska, K]] | |||
[[Category: ISFI, Integrated Center for Structure and Function Innovation]] | |||
[[Category: Dinb superfamily]] | [[Category: Dinb superfamily]] | ||
[[Category: Integrated center for structure and function innovation]] | [[Category: Integrated center for structure and function innovation]] | ||
[[Category: Isfi]] | [[Category: Isfi]] | ||
[[Category: Protein structure initiative | [[Category: PSI, Protein structure initiative]] | ||
[[Category: Structural genomic]] | [[Category: Structural genomic]] | ||
[[Category: Unknown function]] | [[Category: Unknown function]] | ||
Latest revision as of 10:51, 16 March 2022
Crystal structure of putative metal-dependent hydrolase APC36150Crystal structure of putative metal-dependent hydrolase APC36150
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe crystal structure of the dinB gene product from Geobacillus stearothermophilus (GsDinB) is reported at 2.5 A resolution. The dinB gene is one of the DNA-damage-induced genes and the corresponding protein, DinB, is the founding member of a Pfam family with no known function. The protein contains a four-helix up-down-down-up bundle that has previously been described in the literature in three disparate proteins: the enzyme MDMPI (mycothiol-dependent maleylpyruvate isomerase), YfiT and TTHA0303, a member of a small DUF (domain of unknown function). However, a search of the DALI structural database revealed similarities to a further 11 new unpublished structures contributed by structural genomics centers. The sequences of these proteins are quite divergent and represent several Pfam families, yet their structures are quite similar and most (but not all) seem to have the ability to coordinate a metal ion using a conserved histidine-triad motif. The structural similarities of these diverse proteins suggest that a new Pfam clan encompassing the families that share this fold should be created. The proteins that share this fold exhibit four different quaternary structures: monomeric and three different dimeric forms. The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily.,Cooper DR, Grelewska K, Kim CY, Joachimiak A, Derewenda ZS Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Mar 1;66(Pt, 3):219-24. Epub 2010 Feb 23. PMID:20208147[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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