6JX2

Crystal structure of Ketol-acid reductoisomerase from Corynebacterium glutamicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.184 

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This is version 1.3 of the entry. See complete history


Literature

Crystal Structure and Biochemical Characterization of Ketol-Acid Reductoisomerase fromCorynebacterium glutamicum.

Lee, D.Hong, J.Kim, K.J.

(2019) J Agric Food Chem 67: 8527-8535

  • DOI: https://doi.org/10.1021/acs.jafc.9b03262
  • Primary Citation of Related Structures:  
    6JX2

  • PubMed Abstract: 

    l-Valine belongs to the branched-chain amino acids (BCAAs) and is an essential amino acid that is crucial for all living organisms. l-Valine is industrially produced by the nonpathogenic bacterium Corynebacterium glutamicum and is synthesized by the BCAA biosynthetic pathway. Ketol-acid reductoisomerase (KARI) is the second enzyme in the BCAA pathway and catalyzes the conversion of ( S )-2-acetolactate into ( R )-2,3-dihydroxy-isovalerate, or the conversion of ( S )-2-aceto-2-hydroxybutyrate into ( R )-2,3-dihydroxy-3-methylvalerate. To elucidate the enzymatic properties of KARI from C. glutamicum ( Cg KARI), we successfully produced Cg KARI protein and determined its crystal structure in complex with NADP + and two Mg 2+ ions. Based on the complex structure, docking simulations, and site-directed mutagenesis experiments, we revealed that Cg KARI belongs to Class I KARI and identified key residues involved in stabilization of the substrate, metal ions, and cofactor. Furthermore, we confirmed the difference in the binding of metal ions that depended on the conformational change.


  • Organizational Affiliation

    School of Life Sciences, BK21 Plus KNU Creative BioResearch Group , Kyungpook National University , Daehak-ro 80, Buk-ku , Daegu 702-701 , Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ketol-acid reductoisomerase (NADP(+))
A, B, C, D
344Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: ilvCCgl1273cg1437
EC: 1.1.1.86
UniProt
Find proteins for Q57179 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore Q57179 
Go to UniProtKB:  Q57179
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57179
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
I [auth A],
V [auth C],
Y [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
Q [auth B],
R [auth B],
S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
W [auth D],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.949α = 90
b = 90.179β = 90
c = 157.817γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2020-09-09
    Changes: Derived calculations, Structure summary
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description