1G72

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 98: 432-434

  • DOI: 10.1073/pnas.021547498

  • 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 cofac ...

    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.

    Related Citations: 
    • DETERMINATION OF THE GENE SEQUENCE AND THE THREE-DIMENSIONAL STRUCTURE AT 2.4 ANGSTROMS RESOLUTION OF METHANOL DEHYDROGENASE FROM METHYLOPHILUS W3A1
      Xia, Z.,Dai, W.,ZHANG, Y.,WHITE, S.A.,BOYD, G.D.,Mathews, F.S.
      (1996) J.Mol.Biol. 259: 480

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHANOL DEHYDROGENASE HEAVY SUBUNIT
A, C
573Methylophilus methylotrophusMutation(s): 0 
EC: 1.1.2.7
Find proteins for P38539 (Methylophilus methylotrophus)
Go to UniProtKB:  P38539
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
METHANOL DEHYDROGENASE LIGHT SUBUNIT
B, D
69Methylophilus methylotrophusMutation(s): 0 
Gene Names: moxI
EC: 1.1.2.7
Find proteins for P38540 (Methylophilus methylotrophus)
Go to UniProtKB:  P38540
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PQQ
Query on PQQ
Download SDF File 
Download CCD File 
A, C
PYRROLOQUINOLINE QUINONE
C14 H6 N2 O8
MMXZSJMASHPLLR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 98.115α = 90.00
b = 69.744β = 110.29
c = 109.838γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
MERLOTphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance