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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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

    KNU Institute for Microorganisms , Kyungpook National University , Daegu 41566 , Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ketol-acid reductoisomerase (NADP(+))A, B, C, D344Corynebacterium 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , L [auth B] , M [auth B] , N [auth B] , O [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
 Ligand Interaction
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

View Full Validation Report



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