1HW6

CRYSTAL STRUCTURE OF APO-2,5-DIKETO-D-GLUCONATE REDUCTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural assembly of the active site in an aldo-keto reductase by NADPH cofactor.

Sanli, G.Blaber, M.

(2001) J.Mol.Biol. 309: 1209-1218

  • DOI: 10.1006/jmbi.2001.4739

  • PubMed Abstract: 
  • A 1.9 A resolution X-ray structure of the apo-form of Corynebacterium 2,5-diketo-d-gluconic acid reductase A (2,5-DKGR A), a member of the aldo-keto reductase superfamily, has been determined by molecular replacement using the NADPH-bound form of the ...

    A 1.9 A resolution X-ray structure of the apo-form of Corynebacterium 2,5-diketo-d-gluconic acid reductase A (2,5-DKGR A), a member of the aldo-keto reductase superfamily, has been determined by molecular replacement using the NADPH-bound form of the same enzyme as the search model. 2,5-DKGR A catalyzes the NADPH-dependent stereo-specific reduction of 2,5-diketo-d-gluconate (2,5-DKG) to 2-keto-l-gulonate, a precursor in the industrial production of vitamin C. An atomic-resolution structure for the apo-form of the enzyme, in conjunction with our previously reported high-resolution X-ray structure for the holo-enzyme and holo/substrate model, allows a comparative analysis of structural changes that accompany cofactor binding. The results show that regions of the active site undergo coordinated conformational changes of up to 8 A. These conformational changes result in the organization and structural rearrangement of residues associated with substrate binding and catalysis. Thus, NADPH functions not only to provide a hydride ion for catalytic reduction, but is also a critical structural component for formation of a catalytically competent form of DKGR A.


    Organizational Affiliation

    Institute of Molecular Biophysics and Department of Chemistry, Florida State University, Tallahassee, FL 32306-4380, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2,5-DIKETO-D-GLUCONIC ACID REDUCTASE
A
278Corynebacterium sp. (strain ATCC 31090)Mutation(s): 0 
Gene Names: dkgA
EC: 1.1.1.346
Find proteins for P06632 (Corynebacterium sp. (strain ATCC 31090))
Go to UniProtKB:  P06632
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.030α = 90.00
b = 53.940β = 90.00
c = 89.750γ = 90.00
Software Package:
Software NamePurpose
MRCHKmodel building
MRCHKphasing
DENZOdata reduction
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-01-09 
  • Released Date: 2001-06-20 
  • Deposition Author(s): Sanli, G., Blaber, M.

Revision History 

  • Version 1.0: 2001-06-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description