The form A structure of an E21Q catalytic mutant of A. thaliana IGPD2 in complex with Mn2+ and a mixture of its substrate, 2R3S-IGP, and an inhibitor, 2S3S-IGP, to 1.12 A resolution

Experimental Data Snapshot

  • Resolution: 1.12 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 

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This is version 1.3 of the entry. See complete history


Crystal Structures Reveal that the Reaction Mechanism of Imidazoleglycerol-Phosphate Dehydratase Is Controlled by Switching Mn(II) Coordination.

Bisson, C.Britton, K.L.Sedelnikova, S.E.Rodgers, H.F.Eadsforth, T.C.Viner, R.C.Hawkes, T.R.Baker, P.J.Rice, D.W.

(2015) Structure 23: 1236-1245

  • DOI: https://doi.org/10.1016/j.str.2015.05.012
  • Primary Citation of Related Structures:  
    4MU0, 4MU1, 4MU3, 4MU4, 4QNJ, 4QNK

  • PubMed Abstract: 

    Imidazoleglycerol-phosphate dehydratase (IGPD) catalyzes the Mn(II)-dependent dehydration of imidazoleglycerol phosphate (IGP) to 3-(1H-imidazol-4-yl)-2-oxopropyl dihydrogen phosphate during biosynthesis of histidine. As part of a program of herbicide design, we have determined a series of high-resolution crystal structures of an inactive mutant of IGPD2 from Arabidopsis thaliana in complex with IGP. The structures represent snapshots of the enzyme trapped at different stages of the catalytic cycle and show how substrate binding triggers a switch in the coordination state of an active site Mn(II) between six- and five-coordinate species. This switch is critical to prime the active site for catalysis, by facilitating the formation of a high-energy imidazolate intermediate. This work not only provides evidence for the molecular processes that dominate catalysis in IGPD, but also describes how the manipulation of metal coordination can be linked to discrete steps in catalysis, demonstrating one way that metalloenzymes exploit the unique properties of metal ions to diversify their chemistry.

  • Organizational Affiliation

    Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Imidazoleglycerol-phosphate dehydratase 2, chloroplastic205Arabidopsis thalianaMutation(s): 1 
Gene Names: At4g14910dl3495cHISN5B
Find proteins for O23346 (Arabidopsis thaliana)
Explore O23346 
Go to UniProtKB:  O23346
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO23346
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IYP

Download Ideal Coordinates CCD File 
E [auth A](2R,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate
C6 H11 N2 O6 P
Query on IG2

Download Ideal Coordinates CCD File 
D [auth A](2S,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate
C6 H11 N2 O6 P
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
C2 H6 O2
Query on MN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.12 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 
  • Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.1α = 90
b = 113.1β = 90
c = 113.1γ = 90
Software Package:
Software NamePurpose
GDAdata collection
XDSdata reduction
XSCALEdata scaling
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2015-07-22
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description