5XM3

Crystal Structure of Methanol dehydrogenase from Methylophaga aminisulfidivorans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT

Cao, T.P.Choi, J.M.Kim, S.W.Lee, S.H.

(2018) J Microbiol 56: 246-254

  • DOI: https://doi.org/10.1007/s12275-018-7483-y
  • Primary Citation of Related Structures:  
    5XM3

  • PubMed Abstract: 

    The first crystal structure of a pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) from a marine methylotrophic bacterium, Methylophaga aminisulfidivorans MP T (MDH Mas ), was determined at 1.7 Å resolution. The active form of MDH Mas (or MDHI Mas ) is a heterotetrameric α 2 β 2 , where each β-subunit assembles on one side of each of the α-subunits, in a symmetrical fashion, so that two β-subunits surround the two PQQ-binding pockets on the α-subunits. The active site consists of a PQQ molecule surrounded by a β-propeller fold for each α-subunit. Interestingly, the PQQ molecules are coordinated by a Mg 2+ ion, instead of the Ca 2+ ion that is commonly found in the terrestrial MDHI, indicating the efficiency of osmotic balance regulation in the high salt environment. The overall interaction of the β-subunits with the α-subunits appears tighter than that of terrestrial homologues, suggesting the efficient maintenance of MDHI Mas integrity in the sea water environment to provide a firm basis for complex formation with MxaJ Mas or Cyt c L . With the help of the features mentioned above, our research may enable the elucidation of the full molecular mechanism of methanol oxidation by taking advantage of marine bacterium-originated proteins in the methanol oxidizing system (mox), including MxaJ, as the attainment of these proteins from terrestrial bacteria for structural studies has not been successful.


  • Organizational Affiliation

    Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju, 61452, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose dehydrogenase
A, C
627Methylophaga aminisulfidivorans MPMutation(s): 0 
Gene Names: MAMP_01209
UniProt
Find proteins for A3FJ48 (Methylophaga aminisulfidivorans MP)
Explore A3FJ48 
Go to UniProtKB:  A3FJ48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3FJ48
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 [cytochrome c] subunit 2
B, D
90Methylophaga aminisulfidivorans MPMutation(s): 0 
Gene Names: MAMP_01202
EC: 1.1.2.7
UniProt
Find proteins for A3FJ51 (Methylophaga aminisulfidivorans MP)
Explore A3FJ51 
Go to UniProtKB:  A3FJ51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3FJ51
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.926α = 90
b = 109.479β = 100.48
c = 95.554γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chosun UniversityKorea, Republic Of2015

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description