4XEH

Apo structure of KARI from Ignisphaera aggregans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ketol-acid reductoisomeraseA343Ignisphaera aggregans DSM 17230Mutation(s): 0 
Gene Names: ilvCIgag_1561
EC: 1.1.1.86 (PDB Primary Data), 1.1.1.383 (UniProt)
UniProt
Find proteins for E0SRA9 (Ignisphaera aggregans (strain DSM 17230 / JCM 13409 / AQ1.S1))
Explore E0SRA9 
Go to UniProtKB:  E0SRA9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.065α = 90
b = 67.482β = 90
c = 112.35γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




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