2F1D

X-Ray Structure of imidazoleglycerol-phosphate dehydratase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure and mechanism of imidazoleglycerol-phosphate dehydratase.

Glynn, S.E., Baker, P.J., Sedelnikova, S.E., Davies, C.L., Eadsforth, T.C., Levy, C.W., Rodgers, H.F., Blackburn, G.M., Hawkes, T.R., Viner, R., Rice, D.W.

(2005) Structure 13: 1809-1817

  • DOI: https://doi.org/10.1016/j.str.2005.08.012
  • Primary Citation of Related Structures:  
    2F1D

  • PubMed Abstract: 

    • The structure of A. thaliana imidazoleglycerol-phosphate dehydratase, an enzyme of histidine biosynthesis and a target for the triazole phosphonate herbicides, has been determined to 3.0 A resolution. The structure is composed of 24 identical subunits arranged in 432 symmetry and shows how the formation of a novel dimanganese cluster is crucial to the assembly of the active 24-mer from an inactive trimeric precursor and to the formation of the active site of the enzyme ...

    The structure of A. thaliana imidazoleglycerol-phosphate dehydratase, an enzyme of histidine biosynthesis and a target for the triazole phosphonate herbicides, has been determined to 3.0 A resolution. The structure is composed of 24 identical subunits arranged in 432 symmetry and shows how the formation of a novel dimanganese cluster is crucial to the assembly of the active 24-mer from an inactive trimeric precursor and to the formation of the active site of the enzyme. Molecular modeling suggests that the substrate is bound to the manganese cluster as an imidazolate moiety that subsequently collapses to yield a diazafulvene intermediate. The mode of imidazolate recognition exploits pseudosymmetry at the active site arising from a combination of the assembly of the particle and the pseudosymmetry present in each subunit as a result of gene duplication. This provides an intriguing example of the role of evolution in the design of Nature's catalysts.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Imidazoleglycerol-phosphate dehydratase 1
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
207Arabidopsis thalianaMutation(s): 0 
Gene Names: HISN5A, At3g22425, MCB17.17
EC: 4.2.1.19
UniProt
Find proteins for P34047 (Arabidopsis thaliana)
Explore P34047 
Go to UniProtKB:  P34047
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34047
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
BA [auth D],
CB [auth M],
EA [auth E],
FB [auth N],
HA [auth F],
BA [auth D],
CB [auth M],
EA [auth E],
FB [auth N],
HA [auth F],
IB [auth O],
KA [auth G],
LB [auth P],
NA [auth H],
QA [auth I],
S [auth A],
TA [auth J],
V [auth B],
WA [auth K],
Y [auth C],
ZA [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
AA [auth D],
AB [auth M],
BB [auth M],
CA [auth E],
DA [auth E],
AA [auth D],
AB [auth M],
BB [auth M],
CA [auth E],
DA [auth E],
DB [auth N],
EB [auth N],
FA [auth F],
GA [auth F],
GB [auth O],
HB [auth O],
IA [auth G],
JA [auth G],
JB [auth P],
KB [auth P],
LA [auth H],
MA [auth H],
OA [auth I],
PA [auth I],
Q [auth A],
R [auth A],
RA [auth J],
SA [auth J],
T [auth B],
U [auth B],
UA [auth K],
VA [auth K],
W [auth C],
X [auth C],
XA [auth L],
YA [auth L],
Z [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.949α = 90
b = 157.949β = 90
c = 479.965γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance