Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 46.88 kDa 
• Atom Count: 3141 
• Residue Count: 360 
• Unique protein chains: 1

1RHY

Crystal structure of Imidazole Glycerol Phosphate Dehydratase

• DOI: 10.2210/pdb1RHY/pdb

• Classification: LYASE
• Organism(s): Cryptococcus neoformans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-11-14 Released: 2004-05-04 
• Deposition Author(s): Sinha, S.C., Chaudhuri, B.N., Burgner, J.W., Yakovleva, G., Davisson, V.J., Smith, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.228 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold

Sinha, S.C., Chaudhuri, B.N., Burgner, J.W., Yakovleva, G., Davisson, V.J., Smith, J.L.

(2004) J Biol Chem 279: 15491-15498

• PubMed: 14724278 
• DOI: 10.1074/jbc.M312733200
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Imidazole glycerol-phosphate dehydratase (IGPD) catalyzes the sixth step of histidine biosynthesis. The enzyme is of fundamental biochemical interest, because it catalyzes removal of a non-acidic hydrogen atom in the dehydration reaction. It is also a potential target for development of herbicides. IGPD is a metalloenzyme in which transition metals induce aggregation and are required for catalysis. Addition of 1 equivalent of Mn(2+)/subunit is shown by analytical ultracentrifugation to induce the formation of 24-mers from trimeric IGPD. Two histidine-rich motifs may participate in metal binding and aggregation. The 2.3-A crystal structure of metal-free trimeric IGPD from the fungus Filobasidiella neoformans reveals a novel fold containing an internal repeat, apparently the result of gene duplication. The 95-residue alpha/beta half-domain occurs in a few other proteins, including the GHMP kinase superfamily (galacto-homoserine-mevalonate-phosphomevalonate), but duplication to form a compact domain has not been seen elsewhere. Conserved residues cluster at two types of sites in the trimer, each site containing a conserved histidine-rich motif. A model is proposed for the intact, active 24-mer in which all highly conserved residues, including the histidine-rich motifs in both the N- and C-terminal halves of the polypeptide, cluster at a common site between trimers. This site is a candidate for the active site and also for metal binding leading to aggregation of trimers. The structure provides a basis for further studies of enzyme function and mechanism and for development of more potent and specific herbicides.

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Imidazole glycerol phosphate dehydratase	A, B	202	Cryptococcus neoformans	Mutation(s): 0  Gene Names: HIS3 EC: 4.2.1.19
Find proteins for P0CO22 (Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565)) Explore P0CO22  Go to UniProtKB:  P0CO22

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EMC	A, B	ETHYL MERCURY ION C2 H5 Hg MJOUBOKSWBMNGQ-UHFFFAOYSA-N
HG	A, B	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	B	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.228 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.275	α = 90
b = 105.275	β = 90
c = 105.275	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SCALEPACK	data scaling
SOLVE	phasing
DM	model building
CNS	refinement
XDS	data reduction
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-14 
• Released Date: 2004-05-04 
Deposition Author(s): Sinha, S.C., Chaudhuri, B.N., Burgner, J.W., Yakovleva, G., Davisson, V.J., Smith, J.L.

Revision History 

• Version 1.0: 2004-05-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2017-10-11
  Changes: Refinement description