2dbr: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(9 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:2dbr.png|left|200px]]


<!--
==Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (P1)==
The line below this paragraph, containing "STRUCTURE_2dbr", creates the "Structure Box" on the page.
<StructureSection load='2dbr' size='340' side='right'caption='[[2dbr]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2dbr]] is a 6 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=2DBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DBR FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.61&#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>
{{STRUCTURE_2dbr|  PDB=2dbr  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbr OCA], [https://pdbe.org/2dbr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dbr RCSB], [https://www.ebi.ac.uk/pdbsum/2dbr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbr ProSAT], [https://www.topsan.org/Proteins/RSGI/2dbr 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/2dbr_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=2dbr 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 (P1)===
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>
The line below this paragraph, {{ABSTRACT_PUBMED_17327673}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2dbr" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 17327673 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_17327673}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2DBR is a 6 chains structure of sequences from [http://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=2DBR OCA].
[[Category: Pyrococcus horikoshii OT3]]
 
[[Category: Akasaka R]]
==Reference==
[[Category: Arai R]]
<ref group="xtra">PMID:17327673</ref><references group="xtra"/>
[[Category: Kinoshita Y]]
[[Category: Glyoxylate reductase]]
[[Category: Shirouzu M]]
[[Category: Pyrococcus horikoshii ot3]]
[[Category: Terada T]]
[[Category: Akasaka, R.]]
[[Category: Uchikubo-Kamo T]]
[[Category: Arai, R.]]
[[Category: Yokoyama S]]
[[Category: Kinoshita, Y.]]
[[Category: Yoshikawa S]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Shirouzu, M.]]
[[Category: Terada, T.]]
[[Category: Uchikubo-Kamo, T.]]
[[Category: Yokoyama, 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]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:04:28 2009''
Retrieved from "https://proteopedia.org/2dbr"