8RS5

Crystal structure of Methanopyrus kandleri malate dehydrogenase mutant 4

• PDB DOI: https://doi.org/10.2210/pdb8RS5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanopyrus kandleri
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-01-24 Released: 2024-07-10 
• Deposition Author(s): Coquille, S., Engilberge, S., Madern, D.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.283 
• R-Value Work: 0.258 
• R-Value Observed: 0.259 

Starting Model: in silico

Literature

Navigating the conformational landscape of an enzyme. Stabilization of a low populated conformer by evolutionary mutations triggers Allostery into a non-allosteric enzyme.

Coquille, S., Simoes Pereira, C., Brochier-Armanet, C., Roche, J., Santoni, G., Coquelle, N., Girard, E., Sterpone, F., Madern, D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, mass spectrometry, homology

Macromolecule Content

• Total Structure Weight: 70.98 kDa 
• Atom Count: 5,040 
• Modelled Residue Count: 609 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B	317	Methanopyrus kandleri	Mutation(s): 5  Gene Names: mdh, MK1069 EC: 1.1.1.299
UniProt
Find proteins for Q8TWG5 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)) Explore Q8TWG5  Go to UniProtKB:  Q8TWG5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], G [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
K	F [auth A], I [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	D [auth A], E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.283 
• R-Value Work: 0.258 
• R-Value Observed: 0.259 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.15151/ESRF-ES-1041865156

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.36	α = 90
b = 74.36	β = 90
c = 267.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Coquille, S., Engilberge, S., Madern, D.

---

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-16-CE11-0011
Agence Nationale de la Recherche (ANR)	France	ANR-21-CE44-0034-01

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release