1H4I

Methylobacterium extorquens methanol dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Refined Structure of the Quinoprotein Methanol Dehydrogenase from Methylobacterium Extorquens at 1.94 A.

Ghosh, M.Anthony, C.Harlos, K.Goodwin, M.G.Blake, C.

(1995) Structure 3: 177

  • DOI: https://doi.org/10.1016/s0969-2126(01)00148-4
  • Primary Citation of Related Structures:  
    1H4I

  • PubMed Abstract: 

    Methanol dehydrogenase (MDH) is a bacterial periplasmic quinoprotein; it has pyrrolo-quinoline quinone (PQQ) as its prosthetic group, requires Ca2+ for activity and uses cytochrome cL as its electron acceptor. Low-resolution structures of MDH have already been determined. The structure of the alpha 2 beta 2 tetramer of MDH from Methylobacterium extorquens has now been determined at 1.94 A with an R-factor of 19.85%. The alpha-subunit of MDH has an eight-fold radial symmetry, with its eight beta-sheets stabilized by a novel tryptophan docking motif. The PQQ in the active site is held in place by a coplanar tryptophan and by a novel disulphide ring formed between adjacent cysteines which are bonded by an unusual non-planar trans peptide bond. One of the carbonyl oxygens of PQQ is bonded to the Ca2+, probably facilitating attack on the substrate, and the other carbonyl oxygen is out of the plane of the ring, confirming the presence of the predicted free-radical semiquinone form of the prosthetic group.


  • Organizational Affiliation

    Laboratory of Molecular Biophysics, University of Oxford, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METHANOL DEHYDROGENASE SUBUNIT 1
A, C
599Methylorubrum extorquensMutation(s): 0 
UniProt
Find proteins for P16027 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Explore P16027 
Go to UniProtKB:  P16027
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16027
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
METHANOL DEHYDROGENASE SUBUNIT 2
B, D
74Methylorubrum extorquensMutation(s): 0 
EC: 1.1.99.8
UniProt
Find proteins for P14775 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Explore P14775 
Go to UniProtKB:  P14775
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14775
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.16α = 86.21
b = 72.19β = 76.09
c = 86.17γ = 70.44
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance