2IMF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

2-Hydroxychromene-2-carboxylic acid isomerase: a kappa class glutathione transferase from Pseudomonas putida.

Thompson, L.C.Ladner, J.E.Codreanu, S.G.Harp, J.Gilliland, G.L.Armstrong, R.N.

(2007) Biochemistry 46: 6710-6722

  • DOI: https://doi.org/10.1021/bi700356u
  • Primary Citation of Related Structures:  
    2IMD, 2IME, 2IMF

  • PubMed Abstract: 

    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 microM). 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.


  • Organizational Affiliation

    Department of Biochemistry, Center in Molecular Toxicology, and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-hydroxychromene-2-carboxylate isomerase203Pseudomonas putidaMutation(s): 0 
Gene Names: nahD
EC: 2.5.1.18
UniProt
Find proteins for Q51948 (Pseudomonas putida)
Explore Q51948 
Go to UniProtKB:  Q51948
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51948
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH

Download Ideal Coordinates CCD File 
E [auth A]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
CXS
Query on CXS

Download Ideal Coordinates CCD File 
G [auth A]3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
TOM
Query on TOM

Download Ideal Coordinates CCD File 
F [auth A]4-(2-METHOXYPHENYL)-2-OXOBUT-3-ENOIC ACID
C11 H10 O4
QGTBUESLYPYXRT-SREVYHEPSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.533α = 90
b = 75.818β = 90
c = 38.444γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations