4KQX

Mutant Slackia exigua KARI DDV in complex with NAD and an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH.

Brinkmann-Chen, S.Flock, T.Cahn, J.K.Snow, C.D.Brustad, E.M.McIntosh, J.A.Meinhold, P.Zhang, L.Arnold, F.H.

(2013) Proc Natl Acad Sci U S A 110: 10946-10951

  • DOI: 10.1073/pnas.1306073110
  • Primary Citation of Related Structures:  
    4KQW, 4KQX

  • PubMed Abstract: 
  • To date, efforts to switch the cofactor specificity of oxidoreductases from nicotinamide adenine dinucleotide phosphate (NADPH) to nicotinamide adenine dinucleotide (NADH) have been made on a case-by-case basis with varying degrees of success. Here we present a straightforward recipe for altering the cofactor specificity of a class of NADPH-dependent oxidoreductases, the ketol-acid reductoisomerases (KARIs) ...

    To date, efforts to switch the cofactor specificity of oxidoreductases from nicotinamide adenine dinucleotide phosphate (NADPH) to nicotinamide adenine dinucleotide (NADH) have been made on a case-by-case basis with varying degrees of success. Here we present a straightforward recipe for altering the cofactor specificity of a class of NADPH-dependent oxidoreductases, the ketol-acid reductoisomerases (KARIs). Combining previous results for an engineered NADH-dependent variant of Escherichia coli KARI with available KARI crystal structures and a comprehensive KARI-sequence alignment, we identified key cofactor specificity determinants and used this information to construct five KARIs with reversed cofactor preference. Additional directed evolution generated two enzymes having NADH-dependent catalytic efficiencies that are greater than the wild-type enzymes with NADPH. High-resolution structures of a wild-type/variant pair reveal the molecular basis of the cofactor switch.


    Organizational Affiliation

    California Institute of Technology, Pasadena, CA 91125, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ketol-acid reductoisomeraseA, B350Slackia exigua ATCC 700122Mutation(s): 3 
Gene Names: ilvCHMPREF0762_00954
EC: 1.1.1.86
UniProt
Find proteins for D0WGK0 (Slackia exigua (strain ATCC 700122 / DSM 15923 / CIP 105133 / JCM 11022 / KCTC 5966 / S-7))
Explore D0WGK0 
Go to UniProtKB:  D0WGK0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A], J [auth B]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
HIS
Query on HIS

Download Ideal Coordinates CCD File 
K [auth B]HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
 Ligand Interaction
HIO
Query on HIO

Download Ideal Coordinates CCD File 
D [auth A], I [auth B]N-HYDROXY-N-ISOPROPYLOXAMIC ACID
C5 H9 N O4
QVIOSGUKMDGWNN-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],  Q [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.985α = 90
b = 105.346β = 90
c = 122.357γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XSCALEdata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references