3d3x

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[[Image:3d3x.png|left|200px]]
 
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==Crystal structure of botulinum neurotoxin serotype E catalytic domain in complex with SNAP-25 substrate peptide==
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The line below this paragraph, containing "STRUCTURE_3d3x", creates the "Structure Box" on the page.
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<StructureSection load='3d3x' size='340' side='right'caption='[[3d3x]], [[Resolution|resolution]] 2.25&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'>[[3d3x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_butyricum Clostridium butyricum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D3X FirstGlance]. <br>
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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]] 2.25&#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=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_3d3x| PDB=3d3x | 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=3d3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d3x OCA], [https://pdbe.org/3d3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d3x RCSB], [https://www.ebi.ac.uk/pdbsum/3d3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d3x ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9K395_CLOBU Q9K395_CLOBU]
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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/d3/3d3x_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3d3x 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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Clostridium botulinum neurotoxins are the most potent toxins to humans. The recognition and cleavage of SNAREs are prime evente in exhibiting their toxicity. We report here the crystal structure of the catalytically active full-length botulinum serotype E catalytic domain (BoNT E) in complex with SNAP-25 (a SNARE protein) substrate peptide Arg(180)-Ile(181)-Met(182)-Glu(183) (P1-P3'). It is remarkable that the peptide spanning the scissile bond binds to but bypasses cleavage by the enzyme and inhibits the catalysis fairly with K(i) approximately 69 microm. The inhibitory peptide occupies the active site of BoNT E and shows well defined electron density. The catalytic zinc and the conserved key residue Tyr(350) of the enzyme facilitate the docking of Arg(180) (P1) by interacting with its carbonyl oxygen that displaces the nucleophilic water. The general base Glu(212) side chain interacts with the main chain amino group of P1 and P1'. Conserved Arg(347) of BoNT E stabilizes the proper docking of the Ile(181) (P1') main chain, whereas the hydrophobic pockets stabilize the side chains of Ile(181) (P1') and Met(182) (P2'), and the 250 loop stabilizes Glu(183) (P3'). Structural and functional analysis revealed an important role for the P1' residue and S1' pocket in driving substrate recognition and docking at the active site. This study is the first of its kind and rationalizes the substrate cleavage strategy of BoNT E. Also, our complex structure opens up an excellent opportunity of structure-based drug design for this fast acting and extremely toxic high priority BoNT E.
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===Crystal structure of botulinum neurotoxin serotype E catalytic domain in complex with SNAP-25 substrate peptide===
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SNAP-25 substrate peptide (residues 180-183) binds to but bypasses cleavage by catalytically active Clostridium botulinum neurotoxin E.,Agarwal R, Swaminathan S J Biol Chem. 2008 Sep 19;283(38):25944-51. Epub 2008 Jul 25. PMID:18658150<ref>PMID:18658150</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_18658150}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3d3x" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18658150 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18658150}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[3d3x]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_butyricum Clostridium butyricum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D3X OCA].
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==Reference==
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<ref group="xtra">PMID:018658150</ref><references group="xtra"/>
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[[Category: Clostridium butyricum]]
[[Category: Clostridium butyricum]]
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[[Category: Agarwal, R.]]
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[[Category: Large Structures]]
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[[Category: Swaminathan, S.]]
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[[Category: Agarwal R]]
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[[Category: Bont e]]
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[[Category: Swaminathan S]]
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[[Category: Enzyme-substrate complex]]
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[[Category: Hydrolase]]
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[[Category: Hydrolase-hydrolase substrate complex]]
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[[Category: Snap-25]]
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Current revision

Crystal structure of botulinum neurotoxin serotype E catalytic domain in complex with SNAP-25 substrate peptide

PDB ID 3d3x

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