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4h2k

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Revision as of 01:00, 16 November 2017

Crystal structure of the catalytic domain of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae

Structural highlights

4h2k is a 2 chain structure with sequence from Haein. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3isz, 3ic1
Gene:	dapE, HI_0102 (HAEIN)
Activity:	Succinyl-diaminopimelate desuccinylase, with EC number 3.5.1.18
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DAPE_HAEIN] 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. It can only hydrolyze L,L-N-succinyl-diaminopimelic acid (L,L-SDAP) and is inactive toward D,L-, L,D-, and D,D-SDAP.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The 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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bienvenue DL, Gilner DM, Davis RS, Bennett B, Holz RC. Substrate specificity, metal binding properties, and spectroscopic characterization of the DapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae. Biochemistry. 2003 Sep 16;42(36):10756-63. PMID:12962500 doi:http://dx.doi.org/10.1021/bi034845+
↑ Davis R, Bienvenue D, Swierczek SI, Gilner DM, Rajagopal L, Bennett B, Holz RC. Kinetic and spectroscopic characterization of the E134A- and E134D-altered dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae. J Biol Inorg Chem. 2006 Mar;11(2):206-16. Epub 2006 Jan 19. PMID:16421726 doi:10.1007/s00775-005-0071-8
↑ Gillner DM, Bienvenue DL, Nocek BP, Joachimiak A, Zachary V, Bennett B, Holz RC. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae contains two active-site histidine residues. J Biol Inorg Chem. 2009 Jan;14(1):1-10. doi: 10.1007/s00775-008-0418-z. Epub 2008, Aug 19. PMID:18712420 doi:10.1007/s00775-008-0418-z
↑ Nocek B, Starus A, Makowska-Grzyska M, Gutierrez B, Sanchez S, Jedrzejczak R, Mack JC, Olsen KW, Joachimiak A, Holz RC. The dimerization domain in DapE enzymes is required for catalysis. PLoS One. 2014 May 7;9(5):e93593. doi: 10.1371/journal.pone.0093593. eCollection , 2014. PMID:24806882 doi:http://dx.doi.org/10.1371/journal.pone.0093593

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4h2k"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the catalytic domain of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae==
 <StructureSection load='4h2k' size='340' side='right' caption='[[4h2k]], [[Resolution|resolution]] 1.84&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapE, HI_0102 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</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=4h2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h2k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h2k RCSB], [http://www.ebi.ac.uk/pdbsum/4h2k 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=4h2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h2k OCA], [http://pdbe.org/4h2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h2k RCSB], [http://www.ebi.ac.uk/pdbsum/4h2k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h2k ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4h2k" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

4h2k

From Proteopedia

Revision as of 01:00, 16 November 2017

Crystal structure of the catalytic domain of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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