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| | <StructureSection load='3iqd' size='340' side='right'caption='[[3iqd]], [[Resolution|resolution]] 2.80Å' scene=''> | | <StructureSection load='3iqd' size='340' side='right'caption='[[3iqd]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3iqd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/King_scallop King scallop]. 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> | + | <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> |
| - | </td></tr><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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3c7a|3c7a]], [[3c7c|3c7c]], [[3c7d|3c7d]]</div></td></tr>
| + | <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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">odh1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6579 King scallop])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-octopine_dehydrogenase D-octopine dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.11 1.5.1.11] </span></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=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> | | <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> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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>
| + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: D-octopine dehydrogenase]] | |
| - | [[Category: King scallop]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Grieshaber, M K]] | + | [[Category: Pecten maximus]] |
| - | [[Category: Meyer, T]] | + | [[Category: Grieshaber MK]] |
| - | [[Category: Mueller, A]] | + | [[Category: Meyer T]] |
| - | [[Category: Schmitt, L]] | + | [[Category: Mueller A]] |
| - | [[Category: Smits, S H.J]] | + | [[Category: Schmitt L]] |
| - | [[Category: Willbold, D]] | + | [[Category: Smits SHJ]] |
| - | [[Category: Dehydrogenase]]
| + | [[Category: Willbold D]] |
| - | [[Category: Octopine]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
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.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Muller A, Janssen F, Grieshaber MK. Putative reaction mechanism of heterologously expressed octopine dehydrogenase from the great scallop, Pecten maximus (L). FEBS J. 2007 Dec;274(24):6329-39. Epub 2007 Nov 19. PMID:18028427 doi:EJB6151
- ↑ Smits SH, Mueller A, Schmitt L, Grieshaber MK. A structural basis for substrate selectivity and stereoselectivity in octopine dehydrogenase from Pecten maximus. J Mol Biol. 2008 Aug 1;381(1):200-11. Epub 2008 Jun 7. PMID:18599075 doi:10.1016/j.jmb.2008.06.003
- ↑ Smits SH, Meyer T, Mueller A, van Os N, Stoldt M, Willbold D, Schmitt L, Grieshaber MK. Insights into the mechanism of ligand binding to octopine dehydrogenase from Pecten maximus by NMR and crystallography. PLoS One. 2010 Aug 19;5(8):e12312. PMID:20808820 doi:10.1371/journal.pone.0012312
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