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 1.2 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 U S A 98: 432-434

  • DOI: 10.1073/pnas.021547498
  • 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) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHANOL DEHYDROGENASE HEAVY SUBUNITA, C573Methylophilus methylotrophus W3A1Mutation(s): 0 
EC: 1.1.99.8 (PDB Primary Data), 1.1.2.7 (UniProt)
UniProt
Find proteins for P38539 (Methylophilus methylotrophus)
Explore P38539 
Go to UniProtKB:  P38539
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
METHANOL DEHYDROGENASE LIGHT SUBUNITB, D69Methylophilus methylotrophus W3A1Mutation(s): 0 
EC: 1.1.99.8 (PDB Primary Data), 1.1.2.7 (UniProt)
UniProt
Find proteins for P38540 (Methylophilus methylotrophus)
Explore P38540 
Go to UniProtKB:  P38540
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PQQ (Subject of Investigation/LOI)
Query on PQQ

Download Ideal Coordinates CCD File 
F [auth A], H [auth C]PYRROLOQUINOLINE QUINONE
C14 H6 N2 O8
MMXZSJMASHPLLR-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A], G [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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