2q7v: Difference between revisions

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-{{Seed}}
-[[Image:2q7v.png|left|200px]]
-<!--
+==Crystal Structure of Deinococcus Radiodurans Thioredoxin Reductase==
-The line below this paragraph, containing "STRUCTURE_2q7v", creates the "Structure Box" on the page.
+<StructureSection load='2q7v' size='340' side='right'caption='[[2q7v]], [[Resolution|resolution]] 1.90&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'>[[2q7v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q7V 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-{{STRUCTURE_2q7v|  PDB=2q7v  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q7v OCA], [https://pdbe.org/2q7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q7v RCSB], [https://www.ebi.ac.uk/pdbsum/2q7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q7v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9RSY7_DEIRA Q9RSY7_DEIRA]
+== 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/q7/2q7v_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=2q7v ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+This paper describes the cloning, purification, and characterization of thioredoxin (Trx) and thioredoxin reductase (TrxR) and the structure determination of TrxR from the ionizing radiation-tolerant bacterium Deinococcus radiodurans strain R1. The genes from D. radiodurans encoding Trx and TrxR were amplified by PCR, inserted into a pET expression vector, and overexpressed in Escherichia coli. The overexpressed proteins were purified by metal affinity chromatography, and their activity was demonstrated using well-established assays of insulin precipitation (for Trx), 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) reduction, and insulin reduction (for TrxR). In addition, the crystal structure of oxidized TrxR was determined at 1.9-A resolution. The overall structure was found to be very similar to that of E. coli TrxR and homodimeric with both NADPH- and flavin adenine dinucleotide (FAD)-binding domains containing variants of the canonical nucleotide binding fold, the Rossmann fold. The K(m) (5.7 muM) of D. radiodurans TrxR for D. radiodurans Trx was determined and is about twofold higher than that of the E. coli thioredoxin system. However, D. radiodurans TrxR has a much lower affinity for E. coli Trx (K(m), 44.4 muM). Subtle differences in the surface charge and shape of the Trx binding site on TrxR may account for the differences in recognition. Because it has been suggested that TrxR from D. radiodurans may have dual cofactor specificity (can utilize both NADH and NADPH), D. radiodurans TrxR was tested for its ability to utilize NADH as well. Our results show that D. radiodurans TrxR can utilize only NADPH for activity.
-===Crystal Structure of Deinococcus Radiodurans Thioredoxin Reductase===
+Thioredoxin system from Deinococcus radiodurans.,Obiero J, Pittet V, Bonderoff SA, Sanders DA J Bacteriol. 2010 Jan;192(2):494-501. Epub 2009 Nov 20. PMID:19933368<ref>PMID:19933368</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2q7v" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19933368}}, adds the Publication Abstract to the page
+*[[Thioredoxin reductase 3D structures|Thioredoxin reductase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19933368 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19933368}}
+__TOC__
+</StructureSection>
-==About this Structure==
-Q7V is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q7V OCA].
-==Reference==
-<ref group="xtra">PMID:19933368</ref><references group="xtra"/>
 [[Category: Deinococcus radiodurans]]
-[[Category: Thioredoxin-disulfide reductase]]
+[[Category: Large Structures]]
-[[Category: Bonderoff, S A.]]
+[[Category: Bonderoff SA]]
-[[Category: Goertzen, M M.]]
+[[Category: Goertzen MM]]
-[[Category: Obiero, J.]]
+[[Category: Obiero J]]
-[[Category: Sanders, D A.R.]]
+[[Category: Sanders DAR]]
-[[Category: Fad]]
-[[Category: Flavoprotein]]
-[[Category: Oxidoreductase]]
-[[Category: Redox-active center]]
-[[Category: Rossman fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 27 15:21:00 2010''