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PDBsum entry 1rhy

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1rhy
Jmol
Contents
Protein chains
180 a.a. *
Ligands
EMC ×4
SO4 ×5
GOL ×7
ACY ×7
Metals
_HG ×2
Waters ×247
* Residue conservation analysis
PDB id:
1rhy
Name: Lyase
Title: Crystal structure of imidazole glycerol phosphate dehydratas
Structure: Imidazole glycerol phosphate dehydratase. Chain: a, b. Synonym: igpd. Engineered: yes
Source: Filobasidiella neoformans. Organism_taxid: 5207. Gene: his3. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.189     R-free:   0.228
Authors: S.C.Sinha,B.N.Chaudhuri,J.W.Burgner,G.Yakovleva,V.J.Davisson J.L.Smith
Key ref:
S.C.Sinha et al. (2004). Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold. J Biol Chem, 279, 15491-15498. PubMed id: 14724278 DOI: 10.1074/jbc.M312733200
Date:
14-Nov-03     Release date:   04-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0CO22  (HIS7_CRYNJ) -  Imidazoleglycerol-phosphate dehydratase
Seq:
Struc:
202 a.a.
180 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.19  - Imidazoleglycerol-phosphate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
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
Bound ligand (Het Group name = GOL)
matches with 40.00% similarity
= 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     cellular amino acid biosynthetic process   2 terms 
  Biochemical function     lyase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M312733200 J Biol Chem 279:15491-15498 (2004)
PubMed id: 14724278  
 
 
Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold.
S.C.Sinha, B.N.Chaudhuri, J.W.Burgner, G.Yakovleva, V.J.Davisson, J.L.Smith.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Polypeptide fold of IGPD. The stereo ribbon diagram is color-ramped from blue at the N terminus to red at the C terminus. Secondary structures are labeled as are their terminal residues. This figure and other molecular illustrations were made using MolScript (37) and Raster3D (38).
Figure 3.
FIG. 3. The IGPD half-domain in other proteins. The C-terminal half-domain of IGPD (gray) and the N-terminal region of mevalonate kinase (yellow) (Protein Data Bank 1KVK [PDB] ) are superimposed in this stereo C[ ]trace. All atoms are shown for side chains of conserved residues in the C-terminal (D/N)XHHXXE motif of IGPD, along with a sulfate ion from the crystallization solution. The N-terminal domain of mevalonate kinase binds ATP such that the ATP -phosphate and the sulfate ion in IGPD are in analogous positions at a helix N terminus. Atomic coloring (red, oxygen; blue, nitrogen; magenta, phosphorus; green, sulfur) is used for atomic details with gray carbon for IGPD and yellow carbon for mevalonate kinase. Residue numbers at the polypeptide termini are indicated.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 15491-15498) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19565337 J.Lipchock, and J.P.Loria (2009).
Millisecond dynamics in the allosteric enzyme imidazole glycerol phosphate synthase (IGPS) from Thermotoga maritima.
  J Biomol NMR, 45, 73-84.  
18927256 K.Struhl (2008).
The hisB463 mutation and expression of a eukaryotic protein in Escherichia coli.
  Genetics, 180, 709-714.  
15849257 R.E.Amaro, R.S.Myers, V.J.Davisson, and Z.A.Luthey-Schulten (2005).
Structural elements in IGP synthase exclude water to optimize ammonia transfer.
  Biophys J, 89, 475-487.  
16338409 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, and D.W.Rice (2005).
Structure and mechanism of imidazoleglycerol-phosphate dehydratase.
  Structure, 13, 1809-1817.
PDB code: 2f1d
  16511155 S.E.Glynn, P.J.Baker, S.E.Sedelnikova, C.W.Levy, H.F.Rodgers, J.Blank, T.R.Hawkes, and D.W.Rice (2005).
Purification, crystallization and preliminary crystallographic analysis of Arabidopsis thaliana imidazoleglycerol-phosphate dehydratase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 776-778.  
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 code is shown on the right.