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4onw

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Revision as of 07:34, 25 January 2023

Crystal structure of the catalytic domain of DapE protein from V.cholerea

Structural highlights

4onw is a 2 chain structure with sequence from Vibrio cholerae O1 biovar El Tor str. N16961. This structure supersedes the now removed PDB entry 3t68. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
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]

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^[1]

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

References

↑ 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/4onw"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the catalytic domain of DapE protein from V.cholerea==
-<StructureSection load='4onw' size='340' side='right' caption='[[4onw]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
+<StructureSection load='4onw' size='340' side='right'caption='[[4onw]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4onw]] 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=3t68 3t68]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ONW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ONW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4onw]] 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=3t68 3t68]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ONW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ONW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <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></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <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></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3isz|3isz]]</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=4onw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4onw OCA], [https://pdbe.org/4onw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4onw RCSB], [https://www.ebi.ac.uk/pdbsum/4onw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4onw ProSAT]</span></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='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=4onw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4onw OCA], [http://pdbe.org/4onw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4onw RCSB], [http://www.ebi.ac.uk/pdbsum/4onw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4onw ProSAT]</span></td></tr>
 </table>
 == 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 ==
@@ Line 25: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Succinyl-diaminopimelate desuccinylase]]
+[[Category: Large Structures]]
-[[Category: Vibch]]
+[[Category: Vibrio cholerae O1 biovar El Tor str. N16961]]
-[[Category: Anderson, W F]]
+[[Category: Anderson WF]]
-[[Category: Structural genomic]]
+[[Category: Gu M]]
-[[Category: Gu, M]]
+[[Category: Jedrzejczak R]]
-[[Category: Jedrzejczak, R]]
+[[Category: Joachimiak A]]
-[[Category: Joachimiak, A]]
+[[Category: Makowska-Grzyska M]]
-[[Category: Makowska-Grzyska, M]]
+[[Category: Nocek B]]
-[[Category: Nocek, B]]
-[[Category: Aminopeptidase]]
-[[Category: Csgid]]
-[[Category: Dape]]
-[[Category: Hydrolase]]
-[[Category: M20]]
-[[Category: National institute of allergy and infectious disease]]
-[[Category: Niaid]]
-[[Category: Zn binding]]

4onw

From Proteopedia

Revision as of 07:34, 25 January 2023

Crystal structure of the catalytic domain of DapE protein from V.cholerea

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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