3ean: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3ean.jpg|left|200px]]
-<!--
+==Crystal structure of recombinant rat selenoprotein thioredoxin reductase 1 with reduced C-terminal tail==
-The line below this paragraph, containing "STRUCTURE_3ean", creates the "Structure Box" on the page.
+<StructureSection load='3ean' size='340' side='right'caption='[[3ean]], [[Resolution|resolution]] 2.75&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'>[[3ean]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EAN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EAN 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]] 2.75&#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>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-{{STRUCTURE_3ean|  PDB=3ean  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ean FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ean OCA], [https://pdbe.org/3ean PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ean RCSB], [https://www.ebi.ac.uk/pdbsum/3ean PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ean ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRXR1_RAT TRXR1_RAT]
+== 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/ea/3ean_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=3ean ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Selenoproteins contain a highly reactive 21st amino acid selenocysteine (Sec) encoded by recoding of a predefined UGA codon. Because of a lack of selenoprotein supply, high chemical reactivity of Sec, and intricate translation machineries, selenoprotein crystal structures are difficult to obtain. Structural prerequisites for Sec involvement in enzyme catalysis are therefore sparsely known. Here we present the crystal structure of catalytically active rat thioredoxin reductase 1 (TrxR1), revealing surprises at the C-terminal Sec-containing active site in view of previous literature. The oxidized enzyme presents a selenenylsulfide motif in trans-configuration, with the selenium atom of Sec-498 positioned beneath the side chain of Tyr-116, thereby located far from the redox active moieties proposed to be involved in electron transport to the Sec-containing active site. Upon reduction to a selenolthiol motif, the Sec residue moved toward solvent exposure, consistent with its presumed role in reduction of TrxR1 substrates or as target of electrophilic agents inhibiting the enzyme. A Y116I mutation lowered catalytic efficiency in reduction of thioredoxin, but surprisingly increased turnover using 5-hydroxy-1,4-naphthoquinone (juglone) as substrate. The same mutation also decreased sensitivity to inhibition by cisplatin. The results suggest that Tyr-116 plays an important role for catalysis of TrxR1 by interacting with the selenenylsulfide of oxidized TrxR1, thereby facilitating its reduction in the reductive half-reaction of the enzyme. The interaction of a selenenylsulfide with the phenyl ring of a tyrosine, affecting turnover, switch of substrate specificity, and modulation of sensitivity to electrophilic agents, gives important clues into the mechanism of TrxR1, which is a selenoprotein that plays a major role for mammalian cell fate and function. The results also demonstrate that a recombinant selenoprotein TrxR can be produced in high amount and sufficient purity to enable crystal structure determination, which suggests that additional structural studies of these types of proteins are feasible.
-===Crystal structure of recombinant rat selenoprotein thioredoxin reductase 1 with reduced C-terminal tail===
+Crystal structure and catalysis of the selenoprotein thioredoxin reductase 1.,Cheng Q, Sandalova T, Lindqvist Y, Arner ES J Biol Chem. 2009 Feb 6;284(6):3998-4008. Epub 2008 Dec 3. PMID:19054767<ref>PMID:19054767</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ean" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10512699}}, 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 10512699 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10512699}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-EAN is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EAN OCA].
-==Reference==
-High-level expression in Escherichia coli of selenocysteine-containing rat thioredoxin reductase utilizing gene fusions with engineered bacterial-type SECIS elements and co-expression with the selA, selB and selC genes., Arner ES, Sarioglu H, Lottspeich F, Holmgren A, Bock A, J Mol Biol. 1999 Oct 8;292(5):1003-16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10512699 10512699]
 [[Category: Rattus norvegicus]]
-[[Category: Thioredoxin-disulfide reductase]]
+[[Category: Arner E]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+[[Category: Cheng Q]]
-[[Category: Cytoplasm]]
+[[Category: Lindqvist Y]]
-[[Category: Fad]]
+[[Category: Sandalova T]]
-[[Category: Flavoprotein]]
-[[Category: Mammalian thioredoxin reductase 1]]
-[[Category: Nadp]]
-[[Category: Oxidoreductase]]
-[[Category: Phosphoprotein]]
-[[Category: Redox-active center]]
-[[Category: Selenium]]
-[[Category: Selenocysteine]]
-[[Category: Selenoprotein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Dec  5 09:39:16 2008''