3iqd

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{{STRUCTURE_3iqd| PDB=3iqd | SCENE= }}
 
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===Structure of Octopine-dehydrogenase in complex with NADH and Agmatine===
 
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{{ABSTRACT_PUBMED_20808820}}
 
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==Function==
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==Structure of Octopine-dehydrogenase in complex with NADH and Agmatine==
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[[http://www.uniprot.org/uniprot/OCDH_PECMA OCDH_PECMA]] Catalyzes the reverse reaction of octopine dehydrogenation. Acts on L-arginine in preference to other substrates such as canavanine, cysteine, L-alanine, ornithine or norvaline, owing to the presence of the positively charged guanidium group.<ref>PMID:18028427</ref> <ref>PMID:18599075</ref>
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<StructureSection load='3iqd' size='340' side='right'caption='[[3iqd]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3iqd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pecten_maximus Pecten maximus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IQD 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]] 2.8&#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=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></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=3iqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iqd OCA], [https://pdbe.org/3iqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iqd RCSB], [https://www.ebi.ac.uk/pdbsum/3iqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iqd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/OCDH_PECMA OCDH_PECMA] Catalyzes the reverse reaction of octopine dehydrogenation. Acts on L-arginine in preference to other substrates such as canavanine, cysteine, L-alanine, ornithine or norvaline, owing to the presence of the positively charged guanidium group.<ref>PMID:18028427</ref> <ref>PMID:18599075</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/iq/3iqd_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=3iqd 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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Octopine dehydrogenase (OcDH) from the adductor muscle of the great scallop, Pecten maximus, catalyzes the NADH dependent, reductive condensation of L-arginine and pyruvate to octopine, NAD(+), and water during escape swimming and/or subsequent recovery. The structure of OcDH was recently solved and a reaction mechanism was proposed which implied an ordered binding of NADH, L-arginine and finally pyruvate. Here, the order of substrate binding as well as the underlying conformational changes were investigated by NMR confirming the model derived from the crystal structures. Furthermore, the crystal structure of the OcDH/NADH/agmatine complex was determined which suggests a key role of the side chain of L-arginine in protein cataylsis. Thus, the order of substrate binding to OcDH as well as the molecular signals involved in octopine formation can now be described in molecular detail.
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==About this Structure==
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Insights into the mechanism of ligand binding to octopine dehydrogenase from Pecten maximus by NMR and crystallography.,Smits SH, Meyer T, Mueller A, van Os N, Stoldt M, Willbold D, Schmitt L, Grieshaber MK PLoS One. 2010 Aug 19;5(8):e12312. PMID:20808820<ref>PMID:20808820</ref>
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[[3iqd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pecten_maximus Pecten maximus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IQD OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<ref group="xtra">PMID:020808820</ref><references group="xtra"/><references/>
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</div>
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[[Category: D-octopine dehydrogenase]]
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<div class="pdbe-citations 3iqd" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pecten maximus]]
[[Category: Pecten maximus]]
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[[Category: Grieshaber, M K.]]
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[[Category: Grieshaber MK]]
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[[Category: Meyer, T.]]
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[[Category: Meyer T]]
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[[Category: Mueller, A.]]
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[[Category: Mueller A]]
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[[Category: Schmitt, L.]]
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[[Category: Schmitt L]]
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[[Category: Smits, S H.J.]]
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[[Category: Smits SHJ]]
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[[Category: Willbold, D.]]
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[[Category: Willbold D]]
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[[Category: Dehydrogenase]]
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[[Category: Octopine]]
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[[Category: Oxidoreductase]]
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Current revision

Structure of Octopine-dehydrogenase in complex with NADH and Agmatine

PDB ID 3iqd

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