2dbz: Difference between revisions

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-[[Image:2dbz.png|left|200px]]
-{{STRUCTURE_2dbz|  PDB=2dbz  |  SCENE=  }}
+==Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (P61)==
+<StructureSection load='2dbz' size='340' side='right'caption='[[2dbz]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2dbz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DBZ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2dbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbz OCA], [https://pdbe.org/2dbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dbz RCSB], [https://www.ebi.ac.uk/pdbsum/2dbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbz ProSAT], [https://www.topsan.org/Proteins/RSGI/2dbz TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GYAR_PYRHO GYAR_PYRHO]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/2dbz_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2dbz ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== 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.
-===Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (P61)===
+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<ref>PMID:17327673</ref>
-{{ABSTRACT_PUBMED_17327673}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2dbz" style="background-color:#fffaf0;"></div>
-[[2dbz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBZ OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:017327673</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Glyoxylate reductase]]
+[[Category: Large Structures]]
-[[Category: Pyrococcus horikoshii]]
+[[Category: Pyrococcus horikoshii OT3]]
-[[Category: Akasaka, R.]]
+[[Category: Akasaka R]]
-[[Category: Arai, R.]]
+[[Category: Arai R]]
-[[Category: Kinoshita, Y.]]
+[[Category: Kinoshita Y]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[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: Glyoxylate reductase]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Oxidoreductase]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]