7CFX

NAD-soaked Holo-methanol dehydrogenase (MDH) from Methylococcus capsulatus (Bath)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Mechanism of Pyrroloquinoline Quinone-Dependent Hydride Transfer Chemistry from Spectroscopic and High-Resolution X-ray Structural Studies of the Methanol Dehydrogenase from Methylococcus capsulatus (Bath).

Chan, S.I.Chuankhayan, P.Reddy Nareddy, P.K.Tsai, I.K.Tsai, Y.F.Chen, K.H.Yu, S.S.Chen, C.J.

(2021) J Am Chem Soc 143: 3359-3372

  • DOI: https://doi.org/10.1021/jacs.0c11414
  • Primary Citation of Related Structures:  
    7CDL, 7CE5, 7CE9, 7CED, 7CFX

  • PubMed Abstract: 

    The active site of methanol dehydrogenase (MDH) contains a rare disulfide bridge between adjacent cysteine residues. As a vicinal disulfide, the structure is highly strained, suggesting it might work together with the pyrroloquinoline quinone (PQQ) prosthetic group and the Ca 2+ ion in the catalytic turnover during methanol (CH 3 OH) oxidation. We purify MDH from Methylococcus capsulatus (Bath) with the disulfide bridge broken into two thiols. Spectroscopic and high-resolution X-ray crystallographic studies of this form of MDH indicate that the disulfide bridge is redox active. We observe an internal redox process within the holo -MDH that produces a disulfide radical anion concomitant with a companion PQQ radical, as evidenced by an optical absorption at 408 nm and a magnetically dipolar-coupled biradical in the EPR spectrum. These observations are corroborated by electron-density changes between the two cysteine sulfurs of the disulfide bridge as well as between the bound Ca 2+ ion and the O5-C5 bond of the PQQ in the high-resolution X-ray structure. On the basis of these findings, we propose a mechanism for the controlled redistribution of the two electrons during hydride transfer from the CH 3 OH in the alcohol oxidation without formation of the reduced PQQ ethenediol, a biradical mechanism that allows for possible recovery of the hydride for transfer to an external NAD + oxidant in the regeneration of the PQQ cofactor for multiple catalytic turnovers. In support of this mechanism, a steady-state level of the disulfide radical anion is observed during turnover of the MDH in the presence of CH 3 OH and NAD + .


  • Organizational Affiliation

    Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methanol dehydrogenase protein, large subunit573Methylococcus capsulatus str. BathMutation(s): 0 
UniProt
Find proteins for Q60AR6 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore Q60AR6 
Go to UniProtKB:  Q60AR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60AR6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Methanol dehydrogenase [cytochrome c] subunit 272Methylococcus capsulatus str. BathMutation(s): 0 
EC: 1.1.2.7
UniProt
Find proteins for Q60AR3 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore Q60AR3 
Go to UniProtKB:  Q60AR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60AR3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PQQ (Subject of Investigation/LOI)
Query on PQQ

Download Ideal Coordinates CCD File 
BA [auth H]
DA [auth M]
FA [auth N]
R [auth C]
T [auth D]
BA [auth H],
DA [auth M],
FA [auth N],
R [auth C],
T [auth D],
V [auth A],
X [auth B],
Z [auth G]
PYRROLOQUINOLINE QUINONE
C14 H6 N2 O8
MMXZSJMASHPLLR-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth H]
CA [auth M]
EA [auth N]
Q [auth C]
S [auth D]
AA [auth H],
CA [auth M],
EA [auth N],
Q [auth C],
S [auth D],
U [auth A],
W [auth B],
Y [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.901α = 90
b = 211.028β = 90
c = 221.723γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description