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<StructureSection load='4op4' size='340' side='right'caption='[[4op4]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
<StructureSection load='4op4' size='340' side='right'caption='[[4op4]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4op4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibch Vibch]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3t6m 3t6m]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OP4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4op4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae_O1_biovar_El_Tor_str._N16961 Vibrio cholerae O1 biovar El Tor str. N16961]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3t6m 3t6m]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OP4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.651&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3isz|3isz]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4op4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4op4 OCA], [https://pdbe.org/4op4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4op4 RCSB], [https://www.ebi.ac.uk/pdbsum/4op4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4op4 ProSAT]</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://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 ==
[[http://www.uniprot.org/uniprot/DAPE_VIBCH 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]  
[https://www.uniprot.org/uniprot/DAPE_VIBCH 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]
<div style="background-color:#fffaf0;">
== 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<ref>PMID:24806882</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4op4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Succinyl-diaminopimelate desuccinylase]]
[[Category: Vibrio cholerae O1 biovar El Tor str. N16961]]
[[Category: Vibch]]
[[Category: Anderson WF]]
[[Category: Anderson, W F]]
[[Category: Jedrzejczak R]]
[[Category: Structural genomic]]
[[Category: Joachimiak A]]
[[Category: Jedrzejczak, R]]
[[Category: Makowska-Grzyska M]]
[[Category: Joachimiak, A]]
[[Category: Nocek B]]
[[Category: Makowska-Grzyska, M]]
[[Category: Nocek, B]]
[[Category: Aminopeptidase]]
[[Category: Csgid]]
[[Category: Hydrolase]]
[[Category: M20]]
[[Category: National institute of allergy and infectious disease]]
[[Category: Niaid]]

Latest revision as of 15:41, 1 March 2024

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

4op4 is a 2 chain structure with sequence from Vibrio cholerae O1 biovar El Tor str. N16961. This structure supersedes the now removed PDB entry 3t6m. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.651Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

4op4, resolution 1.65Å

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