A novel NAD binding protein revealed by the crystal structure of E. Coli 2,3-diketogulonate reductase (YiaK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


A Novel NAD-binding Protein Revealed by the Crystal Structure of 2,3-Diketo-L-gulonate Reductase (YiaK).

Forouhar, F.Lee, I.Benach, J.Kulkarni, K.Xiao, R.Acton, T.B.Montelione, G.T.Tong, L.

(2004) J Biol Chem 279: 13148-13155

  • DOI: https://doi.org/10.1074/jbc.M313580200
  • Primary Citation of Related Structures:  
    1NXU, 1S20

  • PubMed Abstract: 

    Escherichia coli YiaK catalyzes the reduction of 2,3-diketo-L-gulonate in the presence of NADH. It belongs to a large family of oxidoreductases that is conserved in archaea, bacteria, and eukaryotes but shows no sequence homology to other proteins. We report here the crystal structures at up to 2.0-A resolution of YiaK alone and in complex with NAD-tartrate. YiaK has a new polypeptide backbone fold and a novel mode of recognizing the NAD cofactor. In addition, NAD is bound in an unusual conformation, at the interface of a dimer of the enzyme. The crystallographic analysis unexpectedly revealed the binding of tartrate in the active site. Enzyme kinetics studies confirm that tartrate and the related D-malate are inhibitors of YiaK. In contrast to most other enzymes where substrate binding produces a more closed conformation, the binding of NAD-tartrate to YiaK produces a more open active site. The free enzyme conformation is incompatible with NAD binding. His(44) is likely the catalytic residue of the enzyme.

  • Organizational Affiliation

    Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical oxidoreductase yiaK
A, B, C, D, E
A, B, C, D, E, F, G, H
340Escherichia coliMutation(s): 15 
Gene Names: yiaKb3575
EC: 1.1.1 (PDB Primary Data), (UniProt)
Find proteins for P37672 (Escherichia coli (strain K12))
Explore P37672 
Go to UniProtKB:  P37672
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37672
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth D]
P [auth F]
R [auth G]
J [auth A],
L [auth B],
N [auth D],
P [auth F],
R [auth G],
T [auth H]
C21 H27 N7 O14 P2
Query on TLA

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth D]
O [auth F]
Q [auth G]
I [auth A],
K [auth B],
M [auth D],
O [auth F],
Q [auth G],
S [auth H]
C4 H6 O6
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.524α = 79.55
b = 81.275β = 77.22
c = 113.215γ = 82.01
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection