Experimental Data Snapshot

  • Resolution: 2.4 Å

wwPDB Validation 3D Report Full Report

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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: 480-501

  • PubMed Abstract: 
  • The DNA sequences for the genes encoding the heavy and light subunits of methanol dehydrogenase from Methylophilus methylotrophus W3A1 have been determined. The deduced amino acid sequence has enabled the structure of the enzyme to be refined at 2.4 ...

    The DNA sequences for the genes encoding the heavy and light subunits of methanol dehydrogenase from Methylophilus methylotrophus W3A1 have been determined. The deduced amino acid sequence has enabled the structure of the enzyme to be refined at 2.4 angstrom resolution against X-ray data collected on a Hamlin area detector. The structure was refined using the programs PROFFT and X-PLOR with several model building step interspersed. The final model contains two heavy chains (571 amino acids), two light chains (69 amino acids), two molecules of pyrroloquinoline quinone, two Ca2+ and 521 solvent molecules. Each half molecule contains four disulfide linkages and four cis peptides. One of the disulfides is formed from two adjacent cysteine residues linked by a trans peptide which creates a novel eight-membered ring. The heavy subunit is an 8-fold beta-propeller, each "blade" of which is a four-stranded antiparallel twisted beta-sheet. The light chain is an elongated subunit stretching across the surface of the heavy subunit, with residues 1 to 32 containing four beta-turns and residues 33 to 62 forming a helix; however, it neither interacts with the active site, nor the other HL dimer and its functional role is obscure. Around the 8-fold beta-propeller there is a repeating pattern of tryptophan residues located in the outer strand of seven of the eight beta-leaflets, each packed between adjacent leaflets. Each of these tryptophan residues is centered in the beta-strand and participates in the main chain hydrogen bonding of the sheet. Five of the seven tryptophan residues have closely similar interactions with the adjacent beta-leaflet including stacking of the tryptophan indole rings against a peptide plane and formation of a hydrogen bond from NE1 of the indole ring to a main-chain carbonyl. This repeating pattern is conserved over a number of MEDH sequences. The PQQ is located on the pseudo 8-fold rotation axis of the heavy subunit, in a funnel-shaped internal cavity, sandwiched between the indole ring of Trp237 and the two sulfur atoms of the Cys103-Cys104 vicinal disulfide. A hexacoordinate Ca2+ is bound in the active site by one nitrogen and five oxygen ligands, three from the PQQ and the others from two protein side-chains. In the active site an isolated solvent molecule is bound to the O5 of PQQ and to a nearby aspartate side-chain; its position may be the binding site for methanol. The aspartate might than serve as a general base for proton abstraction from the substrate hydroxyl. The C5 atom of PQQ could be activated by electrophilic catalysis by a nearby argenine side-chain or by the calcium ion bound to PQQ.

    Related Citations: 
    • The Three-Dimensional Structures of Methanol Dehydrogenase from Two Methylotrophic Bacteria at 2.6-A Resolution
      Xia, Z.X.,Dai, W.W.,Xiong, J.P.,Hao, Z.P.,Davidson, V.L.,White, S.,Mathews, F.S.
      (1992) J.Biol.Chem. 267: 22289
    • The Active Site Structure of the Calcium-Containing Quinoprotein Methanol Dehydrogenase
      White, S.,Boyd, G.,Mathews, F.S.,Xia, Z.X.,Dai, W.W.,Zhang, Y.F.,Davidson, V.L.
      (1993) Biochemistry 32: 12955

    Organizational Affiliation

    Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A, C
571Methylophilus methylotrophusMutation(s): 0 
Find proteins for P38539 (Methylophilus methylotrophus)
Go to UniProtKB:  P38539
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
B, D
69Methylophilus methylotrophusMutation(s): 0 
Gene Names: moxI
Find proteins for P38540 (Methylophilus methylotrophus)
Go to UniProtKB:  P38540
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download SDF File 
Download CCD File 
A, C
 Ligand Interaction
Query on PQQ

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Download CCD File 
A, C
C14 H6 N2 O8
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 2.4 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 124.900α = 90.00
b = 62.700β = 93.40
c = 85.000γ = 90.00
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance