5UJK

Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1107/S2053230X18011809
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD + , and ...

    Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) 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

    Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malate dehydrogenase
A
320Methylorubrum extorquensMutation(s): 0 
Gene Names: mdh
EC: 1.1.1.37
Find proteins for Q84FY8 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Go to UniProtKB:  Q84FY8
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2017-01-18 
  • Released Date: 2017-02-08 
  • Deposition Author(s): Gonzalez, J.M.

Revision History 

  • 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