This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1r4w

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:20, 14 February 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1r4w.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of Mitochondrial class kappa glutathione transferase==
-
The line below this paragraph, containing "STRUCTURE_1r4w", creates the "Structure Box" on the page.
+
<StructureSection load='1r4w' size='340' side='right'caption='[[1r4w]], [[Resolution|resolution]] 2.50&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'>[[1r4w]] is a 4 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=1R4W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R4W 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]] 2.5&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene></td></tr>
-
{{STRUCTURE_1r4w| PDB=1r4w | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r4w OCA], [https://pdbe.org/1r4w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r4w RCSB], [https://www.ebi.ac.uk/pdbsum/1r4w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r4w ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/GSTK1_RAT GSTK1_RAT] Might confer protection against genotoxic and cytotoxic electrophiles in the mitochondrial compartment.
 +
== 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/r4/1r4w_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=1r4w ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal structure of Mitochondrial class kappa glutathione transferase'''
+
==See Also==
-
 
+
*[[Glutathione S-transferase 3D structures|Glutathione S-transferase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
The class kappa glutathione (GSH) transferase is an enzyme that resides in the mitochondrial matrix. Its relationship to members of the canonical GSH transferase superfamily has remained an enigma. The three-dimensional structure of the class kappa enzyme from rat (rGSTK1-1) in complex with GSH has been solved by single isomorphous replacement with anomalous scattering at a resolution of 2.5 A. The structure reveals that the enzyme is more closely related to the protein disulfide bond isomerase, dsbA, from Escherichia coli than it is to members of the canonical superfamily. The structures of rGSTK1-1 and the canonical superfamily members indicate that the proteins folds have diverged from a common thioredoxin/glutaredoxin progenitor but did so by different mechanisms. The mitochondrial enzyme, therefore, represents a fourth protein superfamily that supports GSH transferase activity. The thioredoxin domain functions in a manner that is similar to that seen in the canonical enzymes by providing key structural elements for the recognition of GSH. The hydroxyl group of S16 is within hydrogen-bonding distance of the sulfur of bound GSH and is, in part, responsible for the ionization of the thiol in the E*GSH complex (pKa = 6.4 +/- 0.1). Preequilibrium kinetic experiments indicate that the k(on) for GSH is 1 x 10(5) M(-1) s(-1) and k(off) for GS- is approximately 8 s(-1) and relatively slow with respect to turnover with 1-chloro-2, 4-dinitrobenzene (CDNB). As a result, the KM(GSH) (11 mM) is much larger than the apparent Kd(GSH) (90 microM). The active site has a relatively open access channel that is flanked by disordered loops that may explain the relatively high turnover number (280 s(-1) at pH 7.0) toward CDNB. The disordered loops form an extensive contiguous patch on one face of the dimeric enzyme, a fact that suggests that the protein surface may interact with a membrane or other protein partner.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1R4W is a [[Single protein]] structure of sequence 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=1R4W OCA].
+
-
 
+
-
==Reference==
+
-
Parallel evolutionary pathways for glutathione transferases: structure and mechanism of the mitochondrial class kappa enzyme rGSTK1-1., Ladner JE, Parsons JF, Rife CL, Gilliland GL, Armstrong RN, Biochemistry. 2004 Jan 20;43(2):352-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14717589 14717589]
+
-
[[Category: Glutathione transferase]]
+
[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
-
[[Category: Single protein]]
+
[[Category: Armstrong RN]]
-
[[Category: Armstrong, R N.]]
+
[[Category: Gilliland GL]]
-
[[Category: Gilliland, G L.]]
+
[[Category: Ladner JE]]
-
[[Category: Ladner, J E.]]
+
[[Category: Parsons JF]]
-
[[Category: Parsons, J F.]]
+
[[Category: Rife CL]]
-
[[Category: Rife, C L.]]
+
-
[[Category: Glutathione transferase]]
+
-
[[Category: Glutathione-s-transferase]]
+
-
[[Category: Kappa gst]]
+
-
[[Category: Rgstk1-1]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:04:44 2008''
+

Current revision

Crystal structure of Mitochondrial class kappa glutathione transferase

PDB ID 1r4w

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1r4w"
Personal tools