2dbq: Difference between revisions

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-{{Seed}}
-[[Image:2dbq.png|left|200px]]
-<!--
+==Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (I41)==
-The line below this paragraph, containing "STRUCTURE_2dbq", creates the "Structure Box" on the page.
+<StructureSection load='2dbq' size='340' side='right'caption='[[2dbq]], [[Resolution|resolution]] 1.70&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'>[[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>
-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]] 1.7&#8491;</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>
-{{STRUCTURE_2dbq|  PDB=2dbq  |  SCENE=  }}
+<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>
+== 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/2dbq_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2dbq 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 (I41)===
+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 2dbq" 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]]
-DBQ is a [[Single protein]] structure of 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=2DBQ OCA].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/17327673 17327673]
-[[Category: Glyoxylate reductase]]
 [[Category: Pyrococcus horikoshii]]
-[[Category: Single protein]]
+[[Category: Akasaka R]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+[[Category: Arai R]]
-[[Category: D-3-phosphoglycerate dehydrogenase]]
+[[Category: Kinoshita Y]]
-[[Category: Glyoxylate reductase]]
+[[Category: Shirouzu M]]
-[[Category: National project on protein structural and functional analyse]]
+[[Category: Terada T]]
-[[Category: Nppsfa]]
+[[Category: Uchikubo-Kamo T]]
-[[Category: Oxidoreductase]]
+[[Category: Yokoyama S]]
-[[Category: Riken structural genomics/proteomics initiative]]
+[[Category: Yoshikawa S]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec  3 20:32:07 2008''