4XDZ

Holo structure of ketol-acid reductoisomerase from Ignisphaera aggregans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 

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:  

  • 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 prese ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ketol-acid reductoisomerase
A, B
343Ignisphaera aggregans (strain DSM 17230 / JCM 13409 / AQ1.S1)Mutation(s): 0 
Gene Names: ilvC
EC: 1.1.1.383
Find proteins for E0SRA9 (Ignisphaera aggregans (strain DSM 17230 / JCM 13409 / AQ1.S1))
Go to UniProtKB:  E0SRA9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

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Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
40E
Query on 40E

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Download CCD File 
A, B
oxo(propan-2-ylamino)acetic acid
C5 H9 N O3
KBMFHCMLHQGQEB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.579α = 90.00
b = 90.753β = 100.25
c = 69.525γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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