2IV2

Reinterpretation of reduced form of formate dehydrogenase H from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Formate-Reduced E. Coli Formate Dehydrogenase H: The Reinterpretation of the Crystal Structure Suggests a New Reaction Mechanism.

Raaijmakers, H.C.A.Romao, M.J.

(2006) J Biol Inorg Chem 11: 849

  • DOI: 10.1007/s00775-006-0129-2
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Re-evaluation of the crystallographic data of the molybdenum-containing E. coli formate dehydrogenase H (Boyington et al. Science 275:1305-1308, 1997), reported in two redox states, reveals important structural differences for the formate-reduced for ...

    Re-evaluation of the crystallographic data of the molybdenum-containing E. coli formate dehydrogenase H (Boyington et al. Science 275:1305-1308, 1997), reported in two redox states, reveals important structural differences for the formate-reduced form, with large implications for the reaction mechanism proposed in that work. We have re-refined the reduced structure with revised protocols and found substantial rearrangement in some parts of it. The original model is essentially correct but an important loop close to the molybdenum active site was mistraced, and, therefore, catalytic relevant residues were located in wrong positions. In particular selenocysteine-140, a ligand of molybdenum in the original work, and essential for catalysis, is no longer bound to the metal after reduction of the enzyme with formate. These results are incompatible with the originally proposed reaction mechanism. On the basis of our new interpretation, we have revised and proposed a new reaction mechanism, which reconciles the new X-ray model with previous biochemical and extended X-ray absorption fine structure data.


    Related Citations: 
    • Crystal Structure of Formate Dehydrogenase H:Catalysis Involving Mo, Molybdopterin, Selenocysteine, and an Fe4S4 Cluster
      Boyington, J.C., Gladyshev, V.N., Khangulov, S.V., Stadtman, T.C., Sun, P.D.
      (1997) Science 275: 1305

    Organizational Affiliation

    REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Monte de Caparica, Portugal.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Formate dehydrogenase HX715Escherichia coliMutation(s): 0 
Gene Names: fdhFb4079JW4040
EC: 1.17.1.9 (PDB Primary Data), 1.17.99.7 (PDB Primary Data)
Find proteins for P07658 (Escherichia coli (strain K12))
Explore P07658 
Go to UniProtKB:  P07658
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2MD
Query on 2MD

Download CCD File 
X
GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER
C20 H28 N10 O13 P2 S2
YDYCAANTTOPADF-JKOCJXFLSA-N
 Ligand Interaction
MGD
Query on MGD

Download CCD File 
X
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
X
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MO
Query on MO

Download CCD File 
X
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download CCD File 
X
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.4α = 90
b = 146.4β = 90
c = 81.27γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-12
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2018-12-19
    Changes: Data collection, Database references, Source and taxonomy, Structure summary