2GSD

NAD-dependent formate dehydrogenase from bacterium Moraxella sp.C2 in complex with NAD and azide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.184 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.142 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NADClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Structures of the apo and holo forms of formate dehydrogenase from the bacterium Moraxella sp. C-1: towards understanding the mechanism of the closure of the interdomain cleft.

Shabalin, I.G.Filippova, E.V.Polyakov, K.M.Sadykhov, E.G.Safonova, T.N.Tikhonova, T.V.Tishkov, V.I.Popov, V.O.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1315-1325

  • DOI: https://doi.org/10.1107/S0907444909040773
  • Primary Citation of Related Structures:  
    2GSD, 3FN4

  • PubMed Abstract: 

    NAD(+)-dependent formate dehydrogenase (FDH) catalyzes the oxidation of formate ion to carbon dioxide coupled with the reduction of NAD(+) to NADH. The crystal structures of the apo and holo forms of FDH from the methylotrophic bacterium Moraxella sp. C-1 (MorFDH) are reported at 1.96 and 1.95 A resolution, respectively. MorFDH is similar to the previously studied FDH from the bacterium Pseudomonas sp. 101 in overall structure, cofactor-binding mode and active-site architecture, but differs in that the eight-residue-longer C-terminal fragment is visible in the electron-density maps of MorFDH. MorFDH also differs in the organization of the dimer interface. The holo MorFDH structure supports the earlier hypothesis that the catalytic residue His332 can form a hydrogen bond to both the substrate and the transition state. Apo MorFDH has a closed conformation of the interdomain cleft, which is unique for an apo form of an NAD(+)-dependent dehydrogenase. A comparison of the structures of bacterial FDH in open and closed conformations allows the differentiation of the conformational changes associated with cofactor binding and domain motion and provides insights into the mechanism of the closure of the interdomain cleft in FDH. The C-terminal residues 374-399 and the substrate (formate ion) or inhibitor (azide ion) binding are shown to play an essential role in the transition from the open to the closed conformation.


  • Organizational Affiliation

    A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, Moscow 119071, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent formate dehydrogenase402Moraxella sp.Mutation(s): 0 
EC: 1.2.1.43 (PDB Primary Data), 1.17.1.9 (UniProt)
UniProt
Find proteins for O08375 (Moraxella sp)
Explore O08375 
Go to UniProtKB:  O08375
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08375
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.184 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.142 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.45α = 90
b = 66.5β = 103.57
c = 75.55γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NADClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-09
    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: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description