4XDY

Structure of NADH-preferring ketol-acid reductoisomerase from an uncultured archean

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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This is version 1.1 of the entry. See complete history. 


Literature

Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases.

Cahn, J.K., Brinkmann-Chen, S., Spatzal, T., Wiig, J.A., Buller, A.R., Einsle, O., Hu, Y., Ribbe, M.W., Arnold, F.H.

(2015) Biochem J 468: 475-484

  • DOI: 10.1042/BJ20150183
  • Primary Citation of Related Structures:  
    4XDY, 4XDZ, 4XEH, 4XIY

  • PubMed Abstract: 

    • Although most sequenced members of the industrially important ketol-acid reductoisomerase (KARI) family are class I enzymes, structural studies to date have focused primarily on the class II KARIs, which arose through domain duplication. In the present study, we present five new crystal structures of class I KARIs ...

    Although most sequenced members of the industrially important ketol-acid reductoisomerase (KARI) family are class I enzymes, structural studies to date have focused primarily on the class II KARIs, which arose through domain duplication. In the present study, we present five new crystal structures of class I KARIs. These include the first structure of a KARI with a six-residue β2αB (cofactor specificity determining) loop and an NADPH phosphate-binding geometry distinct from that of the seven- and 12-residue loops. We also present the first structures of naturally occurring KARIs that utilize NADH as cofactor. These results show insertions in the specificity loops that confounded previous attempts to classify them according to loop length. Lastly, we explore the conformational changes that occur in class I KARIs upon binding of cofactor and metal ions. The class I KARI structures indicate that the active sites close upon binding NAD(P)H, similar to what is observed in the class II KARIs of rice and spinach and different from the opening of the active site observed in the class II KARI of Escherichia coli. This conformational change involves a decrease in the bending of the helix that runs between the domains and a rearrangement of the nicotinamide-binding site.

    Related Citations: 
    • Uncovering rare NADH-preferring ketol-acid reductoisomerases.
      Brinkmann-Chen, S., Cahn, J.K., Arnold, F.H.
      (2014) Metab Eng 26C: 17
    Organizational Affiliation: 

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, U.S.A. frances@cheme.caltech.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ketol-acid reductoisomeraseA, B338uncultured archaeon GZfos26G2Mutation(s): 0 
Gene Names: ilvC, GZ26G2_30
EC: 1.1.1.86 (PDB Primary Data), 1.1.1.382 (UniProt)
UniProt
Find proteins for Q64BR7 (Uncultured archaeon GZfos26G2)
Explore Q64BR7 
Go to UniProtKB:  Q64BR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64BR7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI
Download Ideal Coordinates CCD File 
E [auth A],
L [auth B]		1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N		 Ligand Interaction
HIO
Query on HIO
Download Ideal Coordinates CCD File 
H [auth A],
I [auth B]		N-HYDROXY-N-ISOPROPYLOXAMIC ACID
C5 H9 N O4
QVIOSGUKMDGWNN-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
G [auth A],
N [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth A],
J [auth B],
K [auth B],
C [auth A],
D [auth A],
F [auth A],
J [auth B],
K [auth B],
M [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.695α = 90
b = 141.748β = 90
c = 148.598γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Data collection