4o23

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==Crystal structure of mono-zinc form of succinyl diaminopimelate desuccinylase from Neisseria meningitidis MC58==
==Crystal structure of mono-zinc form of succinyl diaminopimelate desuccinylase from Neisseria meningitidis MC58==
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<StructureSection load='4o23' size='340' side='right' caption='[[4o23]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
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<StructureSection load='4o23' size='340' side='right'caption='[[4o23]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4o23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neimb Neimb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O23 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4o23]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis_MC58 Neisseria meningitidis MC58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O23 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.09&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3isz|3isz]], [[1vgy|1vgy]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapE, NMB1530 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=122586 NEIMB])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4o23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o23 OCA], [https://pdbe.org/4o23 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o23 RCSB], [https://www.ebi.ac.uk/pdbsum/4o23 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o23 ProSAT]</span></td></tr>
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<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>
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<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=4o23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o23 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o23 RCSB], [http://www.ebi.ac.uk/pdbsum/4o23 PDBsum]</span></td></tr>
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</table>
</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DAPE_NEIMB DAPE_NEIMB] 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]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Binding of the competitive inhibitor L-captopril to the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Neisseria meningitidis (NmDapE) was examined by kinetic, spectroscopic, and crystallographic methods. L-Captopril, an angiotensin-converting enzyme (ACE) inhibitor, was previously shown to be a potent inhibitor of the DapE from Haemophilus influenzae (HiDapE) with an IC50 of 3.3 muM and a measured Ki of 1.8 muM and displayed a dose-responsive antibiotic activity toward Escherichia coli. L-Captopril is also a competitive inhibitor of NmDapE with a Ki of 2.8 muM. To examine the nature of the interaction of L-captopril with the dinuclear active site of DapE, we have obtained electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) data for the enzymatically hyperactive Co(II)-substituted forms of both HiDapE and NmDapE. EPR and MCD data indicate that the two Co(II) ions in DapE are antiferromagnetically coupled, yielding an S = 0 ground state, and suggest a thiolate bridge between the two metal ions. Verification of a thiolate-bridged dinuclear complex was obtained by determining the three-dimensional X-ray crystal structure of NmDapE in complex with L-captopril at 1.8 A resolution. Combination of these data provides new insights into binding of L-captopril to the active site of DapE enzymes as well as important inhibitor-active site residue interaction's. Such information is critical for the design of new, potent inhibitors of DapE enzymes.
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Inhibition of the dapE-Encoded N-Succinyl-L,L-diaminopimelic Acid Desuccinylase from Neisseria meningitidis by L-Captopril.,Starus A, Nocek B, Bennett B, Larrabee JA, Shaw DL, Sae-Lee W, Russo MT, Gillner DM, Makowska-Grzyska M, Joachimiak A, Holz RC Biochemistry. 2015 Aug 11;54(31):4834-44. doi: 10.1021/acs.biochem.5b00475. Epub , 2015 Aug 3. PMID:26186504<ref>PMID:26186504</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4o23" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Neimb]]
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[[Category: Large Structures]]
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[[Category: Succinyl-diaminopimelate desuccinylase]]
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[[Category: Neisseria meningitidis MC58]]
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[[Category: Anderson, W F]]
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[[Category: Anderson WF]]
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[[Category: Structural genomic]]
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[[Category: Holz R]]
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[[Category: Holz, R]]
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[[Category: Joachimiak A]]
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[[Category: Joachimiak, A]]
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[[Category: Nocek B]]
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[[Category: Nocek, B]]
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[[Category: Csgid]]
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[[Category: Dape]]
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[[Category: Hydrolase]]
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Current revision

Crystal structure of mono-zinc form of succinyl diaminopimelate desuccinylase from Neisseria meningitidis MC58

PDB ID 4o23

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