PDBsum entry 2f1d

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Lyase PDB id
Protein chains
(+ 10 more) 183 a.a. *
SO4 ×16
_MN ×32
* Residue conservation analysis
PDB id:
Name: Lyase
Title: X-ray structure of imidazoleglycerol-phosphate dehydratase
Structure: Imidazoleglycerol-phosphate dehydratase 1. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p. Synonym: igpd 1. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: 24mer (from PDB file)
3.00Å     R-factor:   0.243     R-free:   0.286
Authors: D.W.Rice,S.E.Glynn,P.J.Baker,S.E.Sedelnikova,C.L.Davies,T.C.
Key ref:
S.E.Glynn et al. (2005). Structure and mechanism of imidazoleglycerol-phosphate dehydratase. Structure, 13, 1809-1817. PubMed id: 16338409 DOI: 10.1016/j.str.2005.08.012
14-Nov-05     Release date:   24-Jan-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P34047  (HIS7A_ARATH) -  Imidazoleglycerol-phosphate dehydratase 1, chloroplastic
270 a.a.
183 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Imidazoleglycerol-phosphate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Histidine Biosynthesis (late stages)
      Reaction: D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2- oxopropyl phosphate + H2O
D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate
= 3-(imidazol-4-yl)-2- oxopropyl phosphate
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     histidine biosynthetic process   1 term 
  Biochemical function     imidazoleglycerol-phosphate dehydratase activity     1 term  


    Added reference    
DOI no: 10.1016/j.str.2005.08.012 Structure 13:1809-1817 (2005)
PubMed id: 16338409  
Structure and mechanism of imidazoleglycerol-phosphate dehydratase.
S.E.Glynn, P.J.Baker, S.E.Sedelnikova, C.L.Davies, T.C.Eadsforth, C.W.Levy, H.F.Rodgers, G.M.Blackburn, T.R.Hawkes, R.Viner, D.W.Rice.
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.
  Selected figure(s)  
Figure 4.
Figure 4. Stereodiagram of the Active Site of A. thaliana IGPD
The protein backbone is shown and colored gold, cyan, and green for chains A, A', and C, respectively. The two manganese ions are shown as labeled purple spheres, and the nonhydrogen atoms of the modeled diazafulvene intermediate are shown in ball-and-stick format and colored by atom, together with the C-2 hydrogen, which is additionally shown and colored yellow. Side chains of residues located within 5 of either of the metal ions or of the diazafulvene are shown in ball-and-stick format and labeled; polar interactions are shown as dashed black lines.
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1809-1817) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16966333 E.S.Rangarajan, A.Proteau, J.Wagner, M.N.Hung, A.Matte, and M.Cygler (2006).
Structural snapshots of Escherichia coli histidinol phosphate phosphatase along the reaction pathway.
  J Biol Chem, 281, 37930-37941.
PDB codes: 2fpr 2fps 2fpu 2fpw 2fpx
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.