2NAD

HIGH RESOLUTION STRUCTURES OF HOLO AND APO FORMATE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High resolution structures of holo and apo formate dehydrogenase.

Lamzin, V.S.Dauter, Z.Popov, V.O.Harutyunyan, E.H.Wilson, K.S.

(1994) J.Mol.Biol. 236: 759-785

  • DOI: 10.1006/jmbi.1994.1188
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Three-dimensional crystal structures of holo (ternary complex enzyme-NAD-azide) and apo NAD-dependent dimeric formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 have been refined to R factors of 11.7% and 14.8% at 2.05 ...

    Three-dimensional crystal structures of holo (ternary complex enzyme-NAD-azide) and apo NAD-dependent dimeric formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 have been refined to R factors of 11.7% and 14.8% at 2.05 and 1.80 A resolution, respectively. The estimated root-mean-square error in atomic co-ordinates is 0.11 A for holo and 0.18 A for apo. X-ray data were collected from single crystals using an imaging plate scanner and synchrotron radiation. In both crystal forms there is a dimer in the asymmetric unit. Both structures show essentially 2-fold molecular symmetry. NAD binding causes movement of the catalytic domain and ordering of the C terminus, where a new helix appears. This completes formation of the enzyme active centre in holo FDH. NAD is bound in the cleft separating the domains and mainly interacts with residues from the co-enzyme binding domain. In apo FDH these residues are held in essentially the same conformation by water molecules occupying the NAD binding region. An azide molecule is located near the point of catalysis, the C4 atom of the nicotinamide moiety of NAD, and overlaps with the proposed formate binding site. There is an extensive channel running from the active site to the protein surface and this is supposed to be used by substrate to reach the active centre after NAD has already bound. The structure of the active site and a hypothetical catalytic mechanism are discussed. Sequence homology of FDH with other NAD-dependent formate dehydrogenases and some D-specific dehydrogenases is discussed on the basis of the FDH three-dimensional structure.


    Related Citations: 
    • Crystal Structure of Nad-Dependent Formate Dehydrogenase
      Lamzin, V.S.,Aleshin, A.E.,Strokopytov, B.V.,Yukhnevich, M.G.,Popov, V.O.,Harutyunyan, E.H.,Wilson, K.S.
      (1992) Eur.J.Biochem. 206: 441


    Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), DESY, Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-DEPENDENT FORMATE DEHYDROGENASE
A, B
393Pseudomonas sp. (strain 101)Mutation(s): 0 
EC: 1.17.1.9
Find proteins for P33160 (Pseudomonas sp. (strain 101))
Go to UniProtKB:  P33160
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
AZI
Query on AZI

Download SDF File 
Download CCD File 
A, B
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NADKi: 100 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 115.970α = 90.00
b = 113.290β = 90.00
c = 63.400γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement
ARP/wARPmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-01-26
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance