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| | ==Structure of dipeptide epimerase from Bacteroides thetaiotaomicron complexed with L-Pro-D-Glu; nonproductive substrate binding.== | | ==Structure of dipeptide epimerase from Bacteroides thetaiotaomicron complexed with L-Pro-D-Glu; nonproductive substrate binding.== |
| - | <StructureSection load='3ijl' size='340' side='right' caption='[[3ijl]], [[Resolution|resolution]] 1.50Å' scene=''> | + | <StructureSection load='3ijl' size='340' side='right'caption='[[3ijl]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ijl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_thetaiotaomicron"_distaso_1912 "bacillus thetaiotaomicron" distaso 1912]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IJL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IJL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ijl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IJL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3iji|3iji]], [[3ijq|3ijq]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BT_1313 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 "Bacillus thetaiotaomicron" Distaso 1912])</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=3ijl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ijl OCA], [https://pdbe.org/3ijl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ijl RCSB], [https://www.ebi.ac.uk/pdbsum/3ijl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ijl ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ijl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ijl OCA], [http://pdbe.org/3ijl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ijl RCSB], [http://www.ebi.ac.uk/pdbsum/3ijl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ijl ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/AEEP_BACTN AEEP_BACTN]] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and may play a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the epimerization of L-Ala-D-Asp, L-Ala-L-Glu, L-Ala-L-Ser, L-Ala-L-Pro, L-Ala-L-L-Val, L-Ala-L-Thr, L-Ala-L-Leu, L-Ala-L-Ile and L-Gly-L-Glu (in vitro).<ref>PMID:22392983</ref> | + | [https://www.uniprot.org/uniprot/AEEP_BACTN AEEP_BACTN] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and may play a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the epimerization of L-Ala-D-Asp, L-Ala-L-Glu, L-Ala-L-Ser, L-Ala-L-Pro, L-Ala-L-L-Val, L-Ala-L-Thr, L-Ala-L-Leu, L-Ala-L-Ile and L-Gly-L-Glu (in vitro).<ref>PMID:22392983</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ij/3ijl_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ij/3ijl_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus thetaiotaomicron distaso 1912]] | + | [[Category: Bacteroides thetaiotaomicron]] |
| - | [[Category: Almo, S C]] | + | [[Category: Large Structures]] |
| - | [[Category: Fedorov, A A]] | + | [[Category: Almo SC]] |
| - | [[Category: Fedorov, E V]] | + | [[Category: Fedorov AA]] |
| - | [[Category: Gerlt, J A]] | + | [[Category: Fedorov EV]] |
| - | [[Category: Lukk, T]] | + | [[Category: Gerlt JA]] |
| - | [[Category: Dipeptide epimerase]] | + | [[Category: Lukk T]] |
| - | [[Category: Enolase superfamily]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: L-pro-d-glu]]
| + | |
| - | [[Category: Nonproductive binding]]
| + | |
| Structural highlights
Function
AEEP_BACTN Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and may play a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the epimerization of L-Ala-D-Asp, L-Ala-L-Glu, L-Ala-L-Ser, L-Ala-L-Pro, L-Ala-L-L-Val, L-Ala-L-Thr, L-Ala-L-Leu, L-Ala-L-Ile and L-Gly-L-Glu (in vitro).[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 PubMed
The rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. Here we describe the results of a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala-Glu epimerases in Eschericiha coli and Bacillus subtilis, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (i) a new group of presumed Ala-Glu epimerases; (ii) several enzymes with specificity for hydrophobic dipeptides, including one from Cytophaga hutchinsonii that epimerizes D-Ala-D-Ala; and (iii) a small group of enzymes that epimerize cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, large-scale fashion.
Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.,Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. Epub 2012 Mar 5. PMID:22392983[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. Epub 2012 Mar 5. PMID:22392983 doi:10.1073/pnas.1112081109
- ↑ Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. Epub 2012 Mar 5. PMID:22392983 doi:10.1073/pnas.1112081109
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