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New page: left|200px<br /><applet load="2dbz" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dbz, resolution 2.45Å" /> '''Crystal Structure of...
 
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[[Image:2dbz.gif|left|200px]]<br /><applet load="2dbz" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2dbz, resolution 2.45&Aring;" />
'''Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (P61)'''<br />


==About this Structure==
==Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (P61)==
2DBZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] with SO4 and NAP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glyoxylate_reductase Glyoxylate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.26 1.1.1.26] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DBZ OCA].
<StructureSection load='2dbz' size='340' side='right'caption='[[2dbz]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
[[Category: Glyoxylate reductase]]
== Structural highlights ==
[[Category: Pyrococcus horikoshii]]
<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>
[[Category: Single protein]]
</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>
[[Category: Akasaka, R.]]
<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>
[[Category: Arai, R.]]
<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>
[[Category: Kamo-Uchikubo, T.]]
</table>
[[Category: Kinoshita, Y.]]
== Function ==
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
[https://www.uniprot.org/uniprot/GYAR_PYRHO GYAR_PYRHO]  
[[Category: Shirouzu, M.]]
== Evolutionary Conservation ==
[[Category: Terada, T.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Yokoyama, S.]]
Check<jmol>
[[Category: Yoshikawa, S.]]
  <jmolCheckbox>
[[Category: NAP]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/2dbz_consurf.spt"</scriptWhenChecked>
[[Category: SO4]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: d-3-phosphoglycerate dehydrogenase]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: glyoxylate reductase]]
  </jmolCheckbox>
[[Category: national project on protein structural and functional analyses]]
</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].
[[Category: nppsfa]]
<div style="clear:both"></div>
[[Category: riken structural genomics/proteomics initiative]]
<div style="background-color:#fffaf0;">
[[Category: rsgi]]
== Publication Abstract from PubMed ==
[[Category: structural genomics]]
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.


''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:31:24 2007''
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2dbz" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus horikoshii OT3]]
[[Category: Akasaka R]]
[[Category: Arai R]]
[[Category: Kinoshita Y]]
[[Category: Shirouzu M]]
[[Category: Terada T]]
[[Category: Uchikubo-Kamo T]]
[[Category: Yokoyama S]]
[[Category: Yoshikawa S]]
Retrieved from "https://proteopedia.org/2dbz"