4op4: Difference between revisions
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==Crystal structure of the catalytic domain of DapE protein from V.cholerea in the Zn bound form== | ==Crystal structure of the catalytic domain of DapE protein from V.cholerea in the Zn bound form== | ||
<StructureSection load='4op4' size='340' side='right' caption='[[4op4]], [[Resolution|resolution]] 1.65Å' scene=''> | <StructureSection load='4op4' size='340' side='right' caption='[[4op4]], [[Resolution|resolution]] 1.65Å' scene=''> | ||
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapE, VC_2152 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243277 VIBCH])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapE, VC_2152 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243277 VIBCH])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinyl-diaminopimelate_desuccinylase Succinyl-diaminopimelate desuccinylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.18 3.5.1.18] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinyl-diaminopimelate_desuccinylase Succinyl-diaminopimelate desuccinylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.18 3.5.1.18] </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=4op4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4op4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4op4 RCSB], [http://www.ebi.ac.uk/pdbsum/4op4 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=4op4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4op4 OCA], [http://pdbe.org/4op4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4op4 RCSB], [http://www.ebi.ac.uk/pdbsum/4op4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4op4 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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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 4op4" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 14:49, 4 August 2016
Crystal structure of the catalytic domain of DapE protein from V.cholerea in the Zn bound formCrystal structure of the catalytic domain of DapE protein from V.cholerea in the Zn bound form
Structural highlights
Function[DAPE_VIBCH] Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls (By similarity).[HAMAP-Rule:MF_01690] Publication Abstract from PubMedThe emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. Therefore dap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) converts N-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. The enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family. To understand the specific role of each domain of the enzyme we engineered dimerization domain deletion mutants of DapEs from Haemophilus influenzae and Vibrio cholerae, and characterized these proteins structurally and biochemically. No activity was observed for all deletion mutants. Structural comparisons of wild-type, inactive monomeric DapE enzymes with other M20 peptidases suggest that the dimerization domain is essential for DapE enzymatic activity. Structural analysis and molecular dynamics simulations indicate that removal of the dimerization domain increased the flexibility of a conserved active site loop that may provide critical interactions with the substrate. The dimerization domain in DapE enzymes is required for catalysis.,Nocek B, Starus A, Makowska-Grzyska M, Gutierrez B, Sanchez S, Jedrzejczak R, Mack JC, Olsen KW, Joachimiak A, Holz RC PLoS One. 2014 May 7;9(5):e93593. doi: 10.1371/journal.pone.0093593. eCollection , 2014. PMID:24806882[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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