3d4m

From Proteopedia

(Difference between revisions)

Current revision

Glutaredoxin 2 oxidized structure

Structural highlights

3d4m is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.05Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLRX2_YEAST Multifunctional enzyme with glutathione-dependent oxidoreductase, glutathione peroxidase and glutathione S-transferase (GST) activity. The disulfide bond functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. In addition, it is also involved in reducing cytosolic protein- and non-protein-disulfides in a coupled system with glutathione reductase. Required for resistance to reactive oxygen species (ROS) by directly reducing hydroperoxides and for the detoxification of ROS-mediated damage.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Glutaredoxins (Grxs) are small (9-12 kDa) heat-stable proteins that are ubiquitously distributed. In Saccharomyces cerevisiae, seven Grx enzymes have been identified. Two of them (yGrx1 and yGrx2) are dithiolic, possessing a conserved Cys-Pro-Tyr-Cys motif. Here, we show that yGrx2 has a specific activity 15 times higher than that of yGrx1, although these two oxidoreductases share 64% identity and 85% similarity with respect to their amino acid sequences. Further characterization of the enzymatic activities through two-substrate kinetics analysis revealed that yGrx2 possesses a lower K(M) for glutathione and a higher turnover than yGrx1. To better comprehend these biochemical differences, the pK(a) of the N-terminal active-site cysteines (Cys27) of these two proteins and of the yGrx2-C30S mutant were determined. Since the pK(a) values of the yGrx1 and yGrx2 Cys27 residues are very similar, these parameters cannot account for the difference observed between their specific activities. Therefore, crystal structures of yGrx2 in the oxidized form and with a glutathionyl mixed disulfide were determined at resolutions of 2.05 and 1.91 A, respectively. Comparisons of yGrx2 structures with the recently determined structures of yGrx1 provided insights into their remarkable functional divergence. We hypothesize that the substitutions of Ser23 and Gln52 in yGrx1 by Ala23 and Glu52 in yGrx2 modify the capability of the active-site C-terminal cysteine to attack the mixed disulfide between the N-terminal active-site cysteine and the glutathione molecule. Mutagenesis studies supported this hypothesis. The observed structural and functional differences between yGrx1 and yGrx2 may reflect variations in substrate specificity.

Structural aspects of the distinct biochemical properties of glutaredoxin 1 and glutaredoxin 2 from Saccharomyces cerevisiae.,Discola KF, de Oliveira MA, Rosa Cussiol JR, Monteiro G, Barcena JA, Porras P, Padilla CA, Guimaraes BG, Netto LE J Mol Biol. 2009 Jan 23;385(3):889-901. Epub 2008 Oct 28. PMID:18992757^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Luikenhuis S, Perrone G, Dawes IW, Grant CM. The yeast Saccharomyces cerevisiae contains two glutaredoxin genes that are required for protection against reactive oxygen species. Mol Biol Cell. 1998 May;9(5):1081-91. PMID:9571241
↑ Collinson EJ, Wheeler GL, Garrido EO, Avery AM, Avery SV, Grant CM. The yeast glutaredoxins are active as glutathione peroxidases. J Biol Chem. 2002 May 10;277(19):16712-7. Epub 2002 Mar 1. PMID:11875065 doi:http://dx.doi.org/10.1074/jbc.M111686200
↑ Collinson EJ, Grant CM. Role of yeast glutaredoxins as glutathione S-transferases. J Biol Chem. 2003 Jun 20;278(25):22492-7. Epub 2003 Apr 8. PMID:12684511 doi:http://dx.doi.org/10.1074/jbc.M301387200
↑ Discola KF, de Oliveira MA, Rosa Cussiol JR, Monteiro G, Barcena JA, Porras P, Padilla CA, Guimaraes BG, Netto LE. Structural aspects of the distinct biochemical properties of glutaredoxin 1 and glutaredoxin 2 from Saccharomyces cerevisiae. J Mol Biol. 2009 Jan 23;385(3):889-901. Epub 2008 Oct 28. PMID:18992757 doi:S0022-2836(08)01340-5

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3d4m"

@@ Line 1: / Line 1: @@
 ==Glutaredoxin 2 oxidized structure==
-<StructureSection load='3d4m' size='340' side='right' caption='[[3d4m]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+<StructureSection load='3d4m' size='340' side='right'caption='[[3d4m]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3d4m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D4M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D4M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3d4m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D4M FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GRX2, TTR, TTR1, YDR513W, D9719.17 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3d4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d4m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d4m RCSB], [http://www.ebi.ac.uk/pdbsum/3d4m PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d4m OCA], [https://pdbe.org/3d4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d4m RCSB], [https://www.ebi.ac.uk/pdbsum/3d4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d4m ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/GLRX2_YEAST GLRX2_YEAST] Multifunctional enzyme with glutathione-dependent oxidoreductase, glutathione peroxidase and glutathione S-transferase (GST) activity. The disulfide bond functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. In addition, it is also involved in reducing cytosolic protein- and non-protein-disulfides in a coupled system with glutathione reductase. Required for resistance to reactive oxygen species (ROS) by directly reducing hydroperoxides and for the detoxification of ROS-mediated damage.<ref>PMID:9571241</ref> <ref>PMID:11875065</ref> <ref>PMID:12684511</ref>
 == 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/d4/3d4m_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d4/3d4m_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3d4m ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3d4m" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Barcena, J A]]
+[[Category: Barcena JA]]
-[[Category: Discola, K F]]
+[[Category: Discola KF]]
-[[Category: Guimaraes, B G]]
+[[Category: Guimaraes BG]]
-[[Category: Netto, L E.S]]
+[[Category: Netto LES]]
-[[Category: Oliveira, M A.de]]
+[[Category: Porras P]]
-[[Category: Porras, P]]
+[[Category: De Oliveira MA]]
-[[Category: Electron transport]]
-[[Category: Grx2]]
-[[Category: Mitochondrion]]
-[[Category: Oxidoreductase]]
-[[Category: Redox-active center]]
-[[Category: Transit peptide]]
-[[Category: Transport]]

3d4m

From Proteopedia

Current revision

Glutaredoxin 2 oxidized structure

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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