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2y7d

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<StructureSection load='2y7d' size='340' side='right'caption='[[2y7d]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
<StructureSection load='2y7d' size='340' side='right'caption='[[2y7d]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2y7d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"candidatus_cloacamonas_acidaminovorans"_pelletier_et_al._2008 "candidatus cloacamonas acidaminovorans" pelletier et al. 2008]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y7D FirstGlance]. <br>
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<table><tr><td colspan='2'>[[2y7d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Cloacimonas_acidaminovorans Candidatus Cloacimonas acidaminovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y7D FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.59&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2y7g|2y7g]], [[2y7e|2y7e]], [[2y7f|2y7f]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2y7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y7d OCA], [https://pdbe.org/2y7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y7d RCSB], [https://www.ebi.ac.uk/pdbsum/2y7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y7d ProSAT]</span></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=2y7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y7d OCA], [https://pdbe.org/2y7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y7d RCSB], [https://www.ebi.ac.uk/pdbsum/2y7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y7d ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/KCE_CLOAI KCE_CLOAI]] Catalyzes the deprotonation of the beta-keto acid, nucleophilic addition onto acetyl-CoA, and intramolecular transfer of the CoA moiety to result in 3-aminobutanoyl-CoA and acetoacetate.<ref>PMID:21632536</ref>
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[https://www.uniprot.org/uniprot/KCE_CLOAI KCE_CLOAI] Catalyzes the deprotonation of the beta-keto acid, nucleophilic addition onto acetyl-CoA, and intramolecular transfer of the CoA moiety to result in 3-aminobutanoyl-CoA and acetoacetate.<ref>PMID:21632536</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The exponential increase in genome sequencing output has led to the accumulation of thousands of predicted genes lacking a proper functional annotation. Among this mass of hypothetical proteins, enzymes catalyzing new reactions, or using novel ways to catalyze already known reactions might still wait to be identified. Here, we provide a structural and biochemical characterization of the 3-keto-5-aminohexanoate cleavage enzyme (Kce), an enzymatic activity long time known as involved in the anaerobic fermentation of lysine, but whose catalytic mechanism has remained elusive so far. Although the enzyme shows the ubiquitous TIM barrel fold and a Zn(2+) cation reminiscent of metal-dependent class II aldolases, our results based on a combination of X-ray snapshots and molecular modelling point to an unprecedented mechanism that proceeds through deprotonation of the 3-keto-5-aminohexanoate substrate, nucleophilic addition onto an incoming acetyl-CoA, intramolecular transfer of the CoA moiety and final retro-Claisen reaction leading to acetoacetate and 3-aminobutyryl-CoA. This model also accounts for earlier observations showing the origin of carbon atoms in the products, as well as the absence of detection of any covalent acyl-enzyme intermediate. Kce is the first representative of a large family of prokaryotic hypothetical proteins, currently annotated as the ''domain of unknown function'' DUF849.
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3-keto-5-aminohexanoate cleavage enzyme: a common fold for an uncommon Claisen-type condensation.,Bellinzoni M, Bastard K, Perret A, Zaparucha A, Perchat N, Vergne C, Wagner T, de Melo-Minardi RC, Artiguenave F, Cohen GN, Weissenbach J, Salanoubat M, Alzari PM J Biol Chem. 2011 Jun 1. PMID:21632536<ref>PMID:21632536</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2y7d" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Candidatus cloacamonas acidaminovorans pelletier et al. 2008]]
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[[Category: Candidatus Cloacimonas acidaminovorans]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Alzari, P M]]
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[[Category: Alzari PM]]
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[[Category: Bellinzoni, M]]
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[[Category: Bellinzoni M]]
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[[Category: Aldolase]]
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[[Category: Lyase]]
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Current revision

Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from Candidatus Cloacamonas acidaminovorans (orthorombic form)

PDB ID 2y7d

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