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3jzu

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{{Seed}}
 
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[[Image:3jzu.jpg|left|200px]]
 
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==Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 complexed with Mg and dipeptide L-Leu-L-Tyr==
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The line below this paragraph, containing "STRUCTURE_3jzu", creates the "Structure Box" on the page.
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<StructureSection load='3jzu' size='340' side='right'caption='[[3jzu]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3jzu]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis_V583 Enterococcus faecalis V583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JZU FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2&#8491;</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=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</scene></td></tr>
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{{STRUCTURE_3jzu| PDB=3jzu | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3jzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jzu OCA], [https://pdbe.org/3jzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jzu RCSB], [https://www.ebi.ac.uk/pdbsum/3jzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jzu ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/HYEP_ENTFA HYEP_ENTFA] Catalyzes the epimerization of L-Ile-L-Tyr to L-Ile-D-Tyr (in vitro). Catalyzes the epimerization of dipeptides, with a preference for substrates with a hydrophobic or basic amino acid in the first position, followed by an aromatic residue in the second position. Has epimerase activity with L-Ile-L-Tyr, L-Val-L-Tyr and L-Arg-L-Tyr (in vitro).<ref>PMID:22392983</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jz/3jzu_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3jzu ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 complexed with Mg and dipeptide L-Leu-L-Tyr===
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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>
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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 3jzu" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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3JZU is a 8 chains structure with sequences from [http://en.wikipedia.org/wiki/Enterococcus_faecalis_v583 Enterococcus faecalis v583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JZU OCA].
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*[[Muconate cycloisomerase|Muconate cycloisomerase]]
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[[Category: Enterococcus faecalis v583]]
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== References ==
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[[Category: Almo, S C.]]
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<references/>
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[[Category: Fedorov, A A.]]
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__TOC__
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[[Category: Fedorov, E V.]]
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</StructureSection>
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[[Category: Gerlt, J A.]]
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[[Category: Enterococcus faecalis V583]]
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[[Category: Imker, H J.]]
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[[Category: Large Structures]]
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[[Category: Sakai, A.]]
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[[Category: Almo SC]]
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[[Category: Dipeptide epimerase]]
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[[Category: Fedorov AA]]
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[[Category: Dipeptide l-leu-l-tyr]]
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[[Category: Fedorov EV]]
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[[Category: Enolase superfamily]]
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[[Category: Gerlt JA]]
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[[Category: Isomerase]]
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[[Category: Imker HJ]]
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[[Category: Sakai A]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 18 11:42:02 2010''
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Current revision

Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 complexed with Mg and dipeptide L-Leu-L-Tyr

PDB ID 3jzu

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