4KQX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 

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.USA 110: 10946-10951

  • DOI: 10.1073/pnas.1306073110
  • Primary Citation of Related Structures:  

  • 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 w ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ketol-acid reductoisomerase
A, B
350Slackia exigua (strain ATCC 700122 / DSM 15923 / CIP 105133 / JCM 11022 / KCTC 5966 / S-7)Mutation(s): 3 
Gene Names: ilvC
EC: 1.1.1.86
Find proteins for D0WGK0 (Slackia exigua (strain ATCC 700122 / DSM 15923 / CIP 105133 / JCM 11022 / KCTC 5966 / S-7))
Go to UniProtKB:  D0WGK0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HIO
Query on HIO

Download SDF File 
Download CCD File 
A, B
N-HYDROXY-N-ISOPROPYLOXAMIC ACID
C5 H9 N O4
QVIOSGUKMDGWNN-UHFFFAOYSA-N
 Ligand Interaction
HIS
Query on HIS

Download SDF File 
Download CCD File 
B
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.985α = 90.00
b = 105.346β = 90.00
c = 122.357γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XSCALEdata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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