Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD

Experimental Data Snapshot

  • Resolution: 1.53 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.126 

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Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase.

Gonzalez, J.M.Marti-Arbona, R.Chen, J.C.H.Broom-Peltz, B.Unkefer, C.J.

(2018) Acta Crystallogr F Struct Biol Commun 74: 610-616

  • DOI: https://doi.org/10.1107/S2053230X18011809
  • Primary Citation of Related Structures:  
    5UJK, 5ULV

  • PubMed Abstract: 

    Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD + , and a ternary complex of MDH and oxaloacetate with ADP-ribose occupying the pyridine nucleotide-binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate-binding site is accessible in the enzyme resting state or NAD + -bound forms, the substrate-bound form exhibits a closed conformation. This conformational change involves the transition of an α-helix to a 3 10 -helix, which causes the adjacent loop to close the active site following coenzyme and substrate binding. In the ternary complex, His284 forms a hydrogen bond to the C2 carbonyl of oxaloacetate, placing it in a position to donate a proton in the formation of (2S)-malate.

  • Organizational Affiliation

    Instituto de Bionanotecnología del NOA, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Santiago del Estero, G4206XCP Santiago del Estero, Argentina.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malate dehydrogenase320Methylorubrum extorquensMutation(s): 0 
Gene Names: mdh
Find proteins for Q84FY8 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Explore Q84FY8 
Go to UniProtKB:  Q84FY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84FY8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.53 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.126 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.189α = 90
b = 108.189β = 90
c = 104.321γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description