3ijq: Difference between revisions
New page: '''Unreleased structure''' The entry 3ijq is ON HOLD Authors: Fedorov, A.A., Fedorov, E.V., Lukk, T., Gerlt, J.A., Almo, S.C. Description: Structure of dipeptide epimerase from Bactero... |
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==Structure of dipeptide epimerase from Bacteroides thetaiotaomicron complexed with L-Ala-D-Glu; productive substrate binding.== | |||
<StructureSection load='3ijq' size='340' side='right'caption='[[3ijq]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ijq]] 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=3IJQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IJQ FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</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=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3ijq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ijq OCA], [https://pdbe.org/3ijq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ijq RCSB], [https://www.ebi.ac.uk/pdbsum/3ijq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ijq ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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 == | |||
[[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/ij/3ijq_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=3ijq ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:22392983</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ijq" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Muconate cycloisomerase|Muconate cycloisomerase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacteroides thetaiotaomicron]] | |||
[[Category: Large Structures]] | |||
[[Category: Almo SC]] | |||
[[Category: Fedorov AA]] | |||
[[Category: Fedorov EV]] | |||
[[Category: Gerlt JA]] | |||
[[Category: Lukk T]] | |||