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| | <StructureSection load='2dbq' size='340' side='right'caption='[[2dbq]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='2dbq' size='340' side='right'caption='[[2dbq]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2dbq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DBQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2dbq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DBQ FirstGlance]. <br> |
| - | </td></tr><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=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.7Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dbr|2dbr]], [[2dbz|2dbz]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH0597 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glyoxylate_reductase Glyoxylate reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.26 1.1.1.26] </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=2dbq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbq OCA], [https://pdbe.org/2dbq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dbq RCSB], [https://www.ebi.ac.uk/pdbsum/2dbq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbq ProSAT], [https://www.topsan.org/Proteins/RSGI/2dbq TOPSAN]</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=2dbq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbq OCA], [https://pdbe.org/2dbq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dbq RCSB], [https://www.ebi.ac.uk/pdbsum/2dbq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbq ProSAT], [https://www.topsan.org/Proteins/RSGI/2dbq TOPSAN]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/GYAR_PYRHO GYAR_PYRHO] |
| | == 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: Pyrococcus shinkaii]] | |
| - | [[Category: Glyoxylate reductase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Akasaka, R]] | + | [[Category: Pyrococcus horikoshii]] |
| - | [[Category: Arai, R]] | + | [[Category: Akasaka R]] |
| - | [[Category: Kinoshita, Y]] | + | [[Category: Arai R]] |
| - | [[Category: Structural genomic]] | + | [[Category: Kinoshita Y]] |
| - | [[Category: Shirouzu, M]] | + | [[Category: Shirouzu M]] |
| - | [[Category: Terada, T]] | + | [[Category: Terada T]] |
| - | [[Category: Uchikubo-Kamo, T]] | + | [[Category: Uchikubo-Kamo T]] |
| - | [[Category: Yokoyama, S]] | + | [[Category: Yokoyama S]] |
| - | [[Category: Yoshikawa, S]] | + | [[Category: Yoshikawa S]] |
| - | [[Category: D-3-phosphoglycerate dehydrogenase]]
| + | |
| - | [[Category: National project on protein structural and functional analyse]]
| + | |
| - | [[Category: Nppsfa]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| Structural highlights
2dbq is a 1 chain structure with sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.7Å |
| Ligands: | , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN |
Function
GYAR_PYRHO
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
Glyoxylate reductase catalyzes the NAD(P)H-linked reduction of glyoxylate to glycolate. Here, the 1.7 A crystal structure of glyoxylate reductase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate [NADP(H)] determined by the single-wavelength anomalous dispersion (SAD) method is reported. The monomeric structure comprises the two domains typical of NAD(P)-dependent dehydrogenases: the substrate-binding domain (SBD) and the nucleotide-binding domain (NBD). The crystal structure and analytical ultracentrifugation results revealed dimer formation. In the NADP(H)-binding site, the pyrophosphate moiety and the 2'-phosphoadenosine moiety are recognized by the glycine-rich loop (residues 157-162) and by loop residues 180-182, respectively. Furthermore, the present study revealed that P. horikoshii glyoxylate reductase contains aromatic clusters and has a larger number of ion pairs and a lower percentage of hydrophobic accessible surface area than its mesophilic homologues, suggesting its thermostability mechanism.
Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.,Yoshikawa S, Arai R, Kinoshita Y, Uchikubo-Kamo T, Wakamatsu T, Akasaka R, Masui R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):357-65. Epub 2007, Feb 21. PMID:17327673[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yoshikawa S, Arai R, Kinoshita Y, Uchikubo-Kamo T, Wakamatsu T, Akasaka R, Masui R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S. Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate. Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):357-65. Epub 2007, Feb 21. PMID:17327673 doi:http://dx.doi.org/10.1107/S0907444906055442
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