3q4d: Difference between revisions
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==Crystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Ala== | ==Crystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Ala== | ||
<StructureSection load='3q4d' size='340' side='right' caption='[[3q4d]], [[Resolution|resolution]] 3.00Å' scene=''> | <StructureSection load='3q4d' size='340' side='right' caption='[[3q4d]], [[Resolution|resolution]] 3.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3q4d]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3q4d]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Cyth3 Cyth3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q4D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3Q4D 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=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | </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=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3q45|3q45]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3q45|3q45]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CHU2140, CHU_2140, tfdD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CHU2140, CHU_2140, tfdD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269798 CYTH3])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chloromuconate_cycloisomerase Chloromuconate cycloisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.5.1.7 5.5.1.7] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chloromuconate_cycloisomerase Chloromuconate cycloisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.5.1.7 5.5.1.7] </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=3q4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3q4d RCSB], [http://www.ebi.ac.uk/pdbsum/3q4d PDBsum]</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=3q4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4d OCA], [http://pdbe.org/3q4d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3q4d RCSB], [http://www.ebi.ac.uk/pdbsum/3q4d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3q4d ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/ | [[http://www.uniprot.org/uniprot/AAEP_CYTH3 AAEP_CYTH3]] Catalyzes the epimerization of D-Ala-D-Ala to D-Ala-L-Ala. Has broad substrate specificity and catalyzes the epimerization of a variety of dipeptides containing an N-terminal Ala followed by a hydrophobic or polar residue, such as Val, Ser and Met (in vitro).<ref>PMID:22392983</ref> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3q4d" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Chloromuconate cycloisomerase]] | [[Category: Chloromuconate cycloisomerase]] | ||
[[Category: | [[Category: Cyth3]] | ||
[[Category: Gerlt, J A]] | [[Category: Gerlt, J A]] | ||
[[Category: Lukk, T]] | [[Category: Lukk, T]] | ||
[[Category: Nair, S K]] | [[Category: Nair, S K]] | ||
[[Category: Isomerase]] | [[Category: Isomerase]] | ||
Revision as of 01:54, 5 August 2016
Crystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-AlaCrystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Ala
Structural highlights
Function[AAEP_CYTH3] Catalyzes the epimerization of D-Ala-D-Ala to D-Ala-L-Ala. Has broad substrate specificity and catalyzes the epimerization of a variety of dipeptides containing an N-terminal Ala followed by a hydrophobic or polar residue, such as Val, Ser and Met (in vitro).[1] Publication Abstract from PubMedThe 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 AlsoReferences
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