3des: Difference between revisions
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==Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Phe dipeptide== | ==Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Phe dipeptide== | ||
<StructureSection load='3des' size='340' side='right' caption='[[3des]], [[Resolution|resolution]] 2.30Å' scene=''> | <StructureSection load='3des' size='340' side='right'caption='[[3des]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3des]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3des]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DES FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3deq|3deq]], [[3der|3der]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3deq|3deq]], [[3der|3der]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TM_0006 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TM_0006 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3des FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3des OCA], [https://pdbe.org/3des PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3des RCSB], [https://www.ebi.ac.uk/pdbsum/3des PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3des ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/AEEP_THEMA AEEP_THEMA]] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.<ref>PMID:19000819</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Thema]] | [[Category: Thema]] | ||
[[Category: Almo, S C]] | [[Category: Almo, S C]] | ||
Revision as of 10:57, 9 February 2022
Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Phe dipeptideCrystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Phe dipeptide
Structural highlights
Function[AEEP_THEMA] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.[1] 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 PubMedWe have developed a computational approach to aid the assignment of enzymatic function for uncharacterized proteins that uses homology modeling to predict the structure of the binding site and in silico docking to identify potential substrates. We apply this method to proteins in the functionally diverse enolase superfamily that are homologous to the characterized L-Ala-D/L-Glu epimerase from Bacillus subtilis. In particular, a protein from Thermotoga martima was predicted to have different substrate specificity, which suggests that it has a different, but as yet unknown, biological function. This prediction was experimentally confirmed, resulting in the assignment of epimerase activity for L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His, whereas the enzyme is annotated incorrectly in GenBank as muconate cycloisomerase. Subsequently, crystal structures of the enzyme were determined in complex with three substrates, showing close agreement with the computational models and revealing the structural basis for the observed substrate selectivity. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.,Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP Structure. 2008 Nov;16(11):1668-77. PMID:19000819[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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