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.


2ime

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2ime" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ime, resolution 1.70&Aring;" /> '''2-Hydroxychromene-2-...)
Current revision (09:03, 21 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2ime.jpg|left|200px]]<br /><applet load="2ime" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2ime, resolution 1.70&Aring;" />
 
-
'''2-Hydroxychromene-2-carboxylate Isomerase: a Kappa Class Glutathione-S-Transferase from Pseudomonas putida'''<br />
 
-
==Overview==
+
==2-Hydroxychromene-2-carboxylate Isomerase: a Kappa Class Glutathione-S-Transferase from Pseudomonas putida==
-
The enzyme 2-hydroxychromene-2-carboxylic acid (HCCA) isomerase catalyzes, the glutathione (GSH)-dependent interconversion (Keq = 1.5) of HCCA and, trans-o-hydroxybenzylidene pyruvic acid (tHBPA) in the naphthalene, catabolic pathway of Pseudomonas putida. The dimeric protein binds one, molecule of GSH very tightly (Kd approximately 5 nM) and a second molecule, of GSH with much lower affinity (Kd approximately 2 to 11 muM). The enzyme, is unstable in the absence of GSH. The turnover number in the forward, direction (47 s-1 at 25 degrees C) greatly exceeds off rates for GSH (koff, approximately 10-3 to 10-2 s-1 at 10 degrees C), suggesting that GSH acts, as a tightly bound cofactor in the reaction. The crystal structure of the, enzyme at 1.7 A resolution reveals that the isomerase is closely related, to class kappa GSH transferases. Diffraction quality crystals could only, be obtained in the presence of GSH and HCCA/tHBPA. Clear electron density, is seen for GSH. Electron density for the organic substrates is located, near the GSH and is best modeled to include both HCCA and tHBPA at, occupancies of 0.5 for each. Although there is no electron density, connecting the sulfur of GSH to the organic substrates, the sulfur is, located very close (2.78 A) to C7 of HCCA. Taken together, the results, suggest that the isomerization reaction involves a short-lived covalent, adduct between the sulfur of GSH and C7 of the substrate.
+
<StructureSection load='2ime' size='340' side='right'caption='[[2ime]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2ime]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IME FirstGlance]. <br>
 +
</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=2C2:(2S)-2-HYDROXY-2H-CHROMENE-2-CARBOXYLIC+ACID'>2C2</scene>, <scene name='pdbligand=CXS:3-CYCLOHEXYL-1-PROPYLSULFONIC+ACID'>CXS</scene>, <scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TOH:(3E)-4-(2-HYDROXYPHENYL)-2-OXOBUT-3-ENOIC+ACID'>TOH</scene></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=2ime FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ime OCA], [https://pdbe.org/2ime PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ime RCSB], [https://www.ebi.ac.uk/pdbsum/2ime PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ime ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/NAHD_PSEPU NAHD_PSEPU] Involved in the naphthalene catabolic pathway. Catalyzes the reversible glutathione-dependent isomerization of 2-hydroxychromene-2-carboxylate (HCCA) to trans-O-hydroxybenzylidenepyruvate (THBPA).<ref>PMID:8002605</ref> <ref>PMID:1447127</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/im/2ime_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=2ime ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
2IME is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with PO4, GSH, TOH, 2C2 and CXS as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glutathione_transferase Glutathione transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.18 2.5.1.18] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2IME OCA].
+
*[[Glutathione S-transferase 3D structures|Glutathione S-transferase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
2-Hydroxychromene-2-carboxylic Acid Isomerase: A Kappa Class Glutathione Transferase from Pseudomonas putida(,)(,)., Thompson LC, Ladner JE, Codreanu SG, Harp J, Gilliland GL, Armstrong RN, Biochemistry. 2007 Jun 12;46(23):6710-6722. Epub 2007 May 18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17508726 17508726]
+
__TOC__
-
[[Category: Glutathione transferase]]
+
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Pseudomonas putida]]
[[Category: Pseudomonas putida]]
-
[[Category: Single protein]]
+
[[Category: Armstrong RN]]
-
[[Category: Armstrong, R.N.]]
+
[[Category: Codreanu SG]]
-
[[Category: Codreanu, S.G.]]
+
[[Category: Gilliland GL]]
-
[[Category: Gilliland, G.L.]]
+
[[Category: Harp J]]
-
[[Category: Harp, J.]]
+
[[Category: Ladner JE]]
-
[[Category: Ladner, J.E.]]
+
[[Category: Thompson LC]]
-
[[Category: Thompson, L.C.]]
+
-
[[Category: 2C2]]
+
-
[[Category: CXS]]
+
-
[[Category: GSH]]
+
-
[[Category: PO4]]
+
-
[[Category: TOH]]
+
-
[[Category: glutathione]]
+
-
[[Category: isomerase]]
+
-
[[Category: kappa gst]]
+
-
[[Category: kgst]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 12:22:29 2007''
+

Current revision

2-Hydroxychromene-2-carboxylate Isomerase: a Kappa Class Glutathione-S-Transferase from Pseudomonas putida

PDB ID 2ime

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/2ime"
Personal tools