1G72

CATALYTIC MECHANISM OF QUINOPROTEIN METHANOL DEHYDROGENASE: A THEORETICAL AND X-RAY CRYSTALLOGRAPHIC INVESTIGATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 

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This is version 1.3 of the entry. See complete history


Literature

Catalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation.

Zheng, Y.J.Xia, Z.x.Chen, Z.w.Mathews, F.S.Bruice, T.C.

(2001) Proc Natl Acad Sci U S A 98: 432-434

  • DOI: https://doi.org/10.1073/pnas.98.2.432
  • Primary Citation of Related Structures:  
    1G72

  • PubMed Abstract: 

    The catalytic mechanism of the reductive half reaction of the quinoprotein methanol dehydrogenase (MDH) is believed to proceed either through a hemiketal intermediate or by direct transfer of a hydride ion from the substrate methyl group to the cofactor, pyrroloquinoline quinone (PQQ). A crystal structure of the enzyme-substrate complex of a similar quinoprotein, glucose dehydrogenase, has recently been reported that strongly favors the hydride transfer mechanism in that enzyme. A theoretical analysis and an improved refinement of the 1.9-A resolution crystal structure of MDH from Methylophilus methylotrophus W3A1 in the presence of methanol, reported earlier, indicates that the observed tetrahedral configuration of the C-5 atom of PQQ in that study represents the C-5-reduced form of the cofactor and lends support for a hydride transfer mechanism for MDH.


  • Organizational Affiliation

    DuPont Agriculture Products, Stine-Haskell Research Center, Newark, DE 19714, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METHANOL DEHYDROGENASE HEAVY SUBUNIT
A, C
573Methylophilus methylotrophus W3A1Mutation(s): 0 
EC: 1.1.99.8
UniProt
Find proteins for P38539 (Methylophilus methylotrophus)
Explore P38539 
Go to UniProtKB:  P38539
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38539
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 LIGHT SUBUNIT
B, D
69Methylophilus methylotrophus W3A1Mutation(s): 0 
EC: 1.1.99.8
UniProt
Find proteins for P38540 (Methylophilus methylotrophus)
Explore P38540 
Go to UniProtKB:  P38540
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38540
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.115α = 90
b = 69.744β = 110.29
c = 109.838γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description