3ic1

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{{Seed}}
 
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[[Image:3ic1.png|left|200px]]
 
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==Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae==
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The line below this paragraph, containing "STRUCTURE_3ic1", creates the "Structure Box" on the page.
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<StructureSection load='3ic1' size='340' side='right'caption='[[3ic1]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3ic1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IC1 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.3&#8491;</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_3ic1| PDB=3ic1 | SCENE= }}
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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=3ic1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ic1 OCA], [https://pdbe.org/3ic1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ic1 RCSB], [https://www.ebi.ac.uk/pdbsum/3ic1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ic1 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DAPE_HAEIN 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.<ref>PMID:12962500</ref> <ref>PMID:16421726</ref> <ref>PMID:18712420</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ic/3ic1_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ic1 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. The dapE operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent potential targets for novel antibacterials. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts N-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. Deletion of the dapE gene is lethal to Helicobacter pylori and Mycobacterium smegmatis, indicating that DapE's are essential for cell growth and proliferation. Since there are no similar pathways in humans, inhibitors that target DapE may have selective toxicity against only bacteria. A major limitation in developing antimicrobial agents that target DapE has been the lack of structural information. Herein, we report the high-resolution X-ray crystal structures of the DapE from Haemophilus influenzae with one and two zinc ions bound in the active site, respectively. These two forms show different activity. Based on these newly determined structures, we propose a revised catalytic mechanism of peptide bond cleavage by DapE enzymes. These structures provide important insight into catalytic mechanism of DapE enzymes as well as a structural foundation that is critical for the rational design of DapE inhibitors.
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===Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae===
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Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.,Nocek BP, Gillner DM, Fan Y, Holz RC, Joachimiak A J Mol Biol. 2010 Apr 2;397(3):617-26. Epub 2010 Feb 4. PMID:20138056<ref>PMID:20138056</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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The line below this paragraph, {{ABSTRACT_PUBMED_20138056}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3ic1" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 20138056 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20138056}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3IC1 is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IC1 OCA].
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==Reference==
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<ref group="xtra">PMID:20138056</ref><references group="xtra"/>
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[[Category: Haemophilus influenzae]]
[[Category: Haemophilus influenzae]]
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[[Category: Succinyl-diaminopimelate desuccinylase]]
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[[Category: Large Structures]]
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[[Category: Gillner, D M.]]
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[[Category: Gillner DM]]
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[[Category: Holz, R C.]]
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[[Category: Holz RC]]
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[[Category: Joachimiak, A.]]
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[[Category: Joachimiak A]]
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[[Category: MCSG, Midwest Center for Structural Genomics.]]
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[[Category: Nocek BP]]
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[[Category: Nocek, B P.]]
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[[Category: Amino-acid biosynthesis]]
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[[Category: Cobalt]]
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[[Category: Dape]]
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[[Category: Diaminopimelate biosynthesis]]
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[[Category: Hydrolase]]
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[[Category: Lysine biosynthesis]]
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[[Category: Mcsg]]
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[[Category: Metal-binding]]
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[[Category: Midwest center for structural genomic]]
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[[Category: Protein structure initiative]]
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[[Category: Psi2]]
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[[Category: Structural genomic]]
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[[Category: Succinyl-diaminopimelate desuccinylase]]
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[[Category: Zinc]]
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[[Category: Zn bound]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 7 09:59:51 2010''
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Current revision

Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae

PDB ID 3ic1

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