1QMG

Acetohydroxyacid isomeroreductase complexed with its reaction product dihydroxy-methylvalerate, manganese and ADP-ribose.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Spinach Acetohydroxyacid Isomeroreductase Complexed with its Product of Reaction Dihydroxy-Methylvalerate, Manganese and Adp-Ribose

Thomazeau, K.Dumas, R.Halgand, F.Forest, E.Douce, R.Biou, V.

(2000) Acta Crystallogr.,Sect.D 56: 389

  • DOI: 10.1107/s0907444900001694

  • PubMed Abstract: 
  • Acetohydroxyacid isomeroreductase catalyses a two-step reaction composed of an alkyl migration followed by an NADPH-dependent reduction. Both steps require a divalent cation and the first step has a strong preference for magnesium. Manganese ions are ...

    Acetohydroxyacid isomeroreductase catalyses a two-step reaction composed of an alkyl migration followed by an NADPH-dependent reduction. Both steps require a divalent cation and the first step has a strong preference for magnesium. Manganese ions are highly unfavourable to the reaction: only 3% residual activity is observed in the presence of this cation. Acetohydroxyacid isomeroreductase has been crystallized with its substrate, 2-aceto-2-hydroxybutyrate (AHB), Mn(2+) and NADPH. The 1.6 A resolution electron-density map showed the reaction product (2,3-dihydroxy-3-methylvalerate, DHMV) and a density corresponding to (phospho)-ADP-ribose instead of the whole NADP(+). This is one of the few structures of an enzyme complexed with its reaction product. The structure of this complex was refined to an R factor of 19.3% and an R(free) of 22.5%. The overall structure of the enzyme is very similar to that of the complex with the reaction-intermediate analogue IpOHA [N-hydroxy-N-isopropyloxamate; Biou et al. (1997), EMBO J. 16, 3405-3415]. However, the active site shows some differences: the nicotinamide is cleaved and the surrounding amino acids have rearranged accordingly. Comparison between the structures corresponding to the reaction intermediate and to the end of the reaction allowed the proposal of a reaction scheme. Taking this result into account, the enzyme was crystallized with Ni(2+) and Zn(2+), for which only 0.02% residual activity were measured; however, the crystals of AHB/Zn/NADPH and of AHB/Ni/NADPH also contain the reaction product. Moreover, mass-spectrometry measurements confirmed the -cleavage of nicotinamide.


    Related Citations: 
    • The Crystal Structure of Plant Acetohydroxyacid Isomeroreductase Complexed with its Reaction Product Dihydroxymethylvalerate, Manganese and (Phospho)-Adp-Ribose
      Biou, V.,Dumas, R.,Cohen-Addad, C.,Douce, R.,Job, D.,Pebay-Peyroula, E.
      (1997) Embo J. 16: 3405


    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel (UMR 5045), CNRS/CEA/Université Joseph Fourier, 41 Rue Jules Horowitz, F-38027 Grenoble CEDEX, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACETOHYDROXY-ACID ISOMEROREDUCTASE
A, B, C, D
524Spinacia oleraceaMutation(s): 0 
Gene Names: AHRI
EC: 1.1.1.86
Find proteins for Q01292 (Spinacia oleracea)
Go to UniProtKB:  Q01292
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APX
Query on APX

Download SDF File 
Download CCD File 
A, B, C, D
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHORIBOSE
C15 H29 N5 O17 P3
QHNQLFGTVLWISK-MQSGHBOVSA-O
 Ligand Interaction
MN
Query on MN

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Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DMV
Query on DMV

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Download CCD File 
A, B, C, D
2,3-DIHYDROXY-VALERIANIC ACID
C6 H12 O4
PDGXJDXVGMHUIR-UJURSFKZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 110.800α = 90.00
b = 61.200β = 95.00
c = 161.700γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
MOSFLMdata reduction
X-PLORrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance