3S2Y

Crystal structure of a chromate/uranium reductase from Gluconacetobacter hansenii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.244 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure Determination and Functional Analysis of a Chromate Reductase from Gluconacetobacter hansenii.

Jin, H.Zhang, Y.Buchko, G.W.Varnum, S.M.Robinson, H.Squier, T.C.Long, P.E.

(2012) Plos One 7: e42432-e42432

  • DOI: 10.1371/journal.pone.0042432

  • PubMed Abstract: 
  • Environmental protection through biological mechanisms that aid in the reductive immobilization of toxic metals (e.g., chromate and uranyl) has been identified to involve specific NADH-dependent flavoproteins that promote cell viability. To understan ...

    Environmental protection through biological mechanisms that aid in the reductive immobilization of toxic metals (e.g., chromate and uranyl) has been identified to involve specific NADH-dependent flavoproteins that promote cell viability. To understand the enzyme mechanisms responsible for metal reduction, the enzyme kinetics of a putative chromate reductase from Gluconacetobacter hansenii (Gh-ChrR) was measured and the crystal structure of the protein determined at 2.25 Å resolution. Gh-ChrR catalyzes the NADH-dependent reduction of chromate, ferricyanide, and uranyl anions under aerobic conditions. Kinetic measurements indicate that NADH acts as a substrate inhibitor; catalysis requires chromate binding prior to NADH association. The crystal structure of Gh-ChrR shows the protein is a homotetramer with one bound flavin mononucleotide (FMN) per subunit. A bound anion is visualized proximal to the FMN at the interface between adjacent subunits within a cationic pocket, which is positioned at an optimal distance for hydride transfer. Site-directed substitutions of residues proposed to involve in both NADH and metal anion binding (N85A or R101A) result in 90-95% reductions in enzyme efficiencies for NADH-dependent chromate reduction. In comparison site-directed substitution of a residue (S118A) participating in the coordination of FMN in the active site results in only modest (50%) reductions in catalytic efficiencies, consistent with the presence of a multitude of side chains that position the FMN in the active site. The proposed proximity relationships between metal anion binding site and enzyme cofactors is discussed in terms of rational design principles for the use of enzymes in chromate and uranyl bioremediation.


    Organizational Affiliation

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America. hongjunj@mir.wustl.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chromate reductase
A, B, C, D
199Komagataeibacter hansenii ATCC 23769N/A
Find proteins for D5QFC5 (Komagataeibacter hansenii ATCC 23769)
Go to UniProtKB:  D5QFC5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.244 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 119.677α = 90.00
b = 90.051β = 119.61
c = 95.234γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
AMoREphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-08-22
    Type: Database references