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PDBsum entry 1jul

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Lyase PDB id
1jul
Jmol
Contents
Protein chain
247 a.a. *
Ligands
MES
Waters ×251
* Residue conservation analysis
PDB id:
1jul
Name: Lyase
Title: Indole-3-glycerolphosphate synthase from sulfolobus solfataricus in a second orthorhombic crystal form
Structure: Indole-3-glycerol phosphate synthase. Chain: a. Synonym: igps. Engineered: yes. Other_details: second orthorhombic crystal form
Source: Sulfolobus solfataricus. Organism_taxid: 2287. Strain: m4. Gene: trpc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.176    
Authors: T.R.Knoechel,M.Hennig,A.Merz,B.Darimont,K.Kirschner, J.N.Jansonius
Key ref:
T.R.Knöchel et al. (1996). The crystal structure of indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus in three different crystal forms: effects of ionic strength. J Mol Biol, 262, 502-515. PubMed id: 8893859 DOI: 10.1006/jmbi.1996.0531
Date:
03-May-96     Release date:   07-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q06121  (TRPC_SULSO) -  Indole-3-glycerol phosphate synthase
Seq:
Struc:
248 a.a.
247 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.48  - Indole-3-glycerol-phosphate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Tryptophan Biosynthesis
      Reaction: 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate = 1-C- (3-indolyl)-glycerol 3-phosphate + CO2 + H2O
1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate
= 1-C- (3-indolyl)-glycerol 3-phosphate
+ CO(2)
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1996.0531 J Mol Biol 262:502-515 (1996)
PubMed id: 8893859  
 
 
The crystal structure of indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus in three different crystal forms: effects of ionic strength.
T.R.Knöchel, M.Hennig, A.Merz, B.Darimont, K.Kirschner, J.N.Jansonius.
 
  ABSTRACT  
 
Indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus is a monomeric enzyme with the common (beta/alpha)8-fold. Recently, its three-dimensional structure was solved in an orthorhombic crystal form, grown by using 1.3 M ammonium sulfate as precipitating agent. Here we describe the X-ray structure analysis of two new crystal forms of this enzyme that were obtained at medium and low ionic strength, respectively. Hexagonal crystals with space group P3(1)21 and cell dimensions a = 62.4 A, b = 62.4 A, c = 122.9 A, gamma = 120 degrees grew in 0.1 M Mes buffer at pH 6.0 with 30% polyethylene glycol monomethylether as precipitant and 0.2 M ammonium sulfate as co-precipitant. A second crystal form with space group P2(1)2(1)2(1) and cell constants a = 62.6 A, b = 74.0 A, c = 74.2 A was obtained using polyethylene glycol and ethylene glycol as precipitants in 0.1 M Mes buffer at pH 6.5. Both structures were solved by molecular replacement and refined at 2.5 A and 2.0 A resolution, respectively. Although the global folds are almost identical, alternative conformations are observed in flexible loop regions, mostly stabilized by crystal contacts. In none of the three crystal forms is the so-called phosphate binding site empty, suggesting that this position has high affinity for anions with tetrahedrally arranged oxygen atoms. Differences in ionic strength of the crystallization buffer have only minor effects on number and specificity of intramolecular salt bridges. The crystal packing, on the other hand, seems to be influenced by the ionic strength of the solvent, since the number of intermolecular salt bridges in the low ionic strength crystal forms is significantly higher.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. 2Fo - Fc electron density map of the active center region in crystal form C contoured at 1.0s with the structural model superimposed. The position and orientation of a bound Mes ion is shown. Although the occupancy is incomplete, the terminal sulfonyl group of Mes is well defined. Drawing produced with O (Jones et al., 1991).
Figure 7.
Figure 7. Stereo view of the salt bridge between Arg19 (loop a0-a00) and Asp111 (loop b3-a3), which is strongly supported by the molecular context. In addition to the extensive hydrogen bond network, the cationic guanidinyl head group of Arg19 interacts with the quadrupolar p-system of Tyr93. The model shown is taken from crystal form C, but the conformation in crystal forms A and B is very similar. The 2Fo - Fc electron density map is contoured at 1.0s. Drawing produced with O (Jones et al., 1991).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 262, 502-515) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17691895 B.Y.Chen, V.Y.Fofanov, D.H.Bryant, B.D.Dodson, D.M.Kristensen, A.M.Lisewski, M.Kimmel, O.Lichtarge, and L.E.Kavraki (2007).
The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.
  J Comput Biol, 14, 791-816.  
15234974 L.Tao, and A.L.Harris (2004).
Biochemical requirements for inhibition of Connexin26-containing channels by natural and synthetic taurine analogs.
  J Biol Chem, 279, 38544-38554.  
11238984 C.Vieille, and G.J.Zeikus (2001).
Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.
  Microbiol Mol Biol Rev, 65, 1.  
9493397 P.M.Dewick (1998).
The biosynthesis of shikimate metabolites.
  Nat Prod Rep, 15, 17-58.  
9578564 P.M.Fitzgerald, J.K.Wu, and J.H.Toney (1998).
Unanticipated inhibition of the metallo-beta-lactamase from Bacteroides fragilis by 4-morpholineethanesulfonic acid (MES): a crystallographic study at 1.85-A resolution.
  Biochemistry, 37, 6791-6800.
PDB code: 1a7t
9893953 R.Scandurra, V.Consalvi, R.Chiaraluce, L.Politi, and P.C.Engel (1998).
Protein thermostability in extremophiles.
  Biochimie, 80, 933-941.  
9166771 M.Hennig, R.Sterner, K.Kirschner, and J.N.Jansonius (1997).
Crystal structure at 2.0 A resolution of phosphoribosyl anthranilate isomerase from the hyperthermophile Thermotoga maritima: possible determinants of protein stability.
  Biochemistry, 36, 6009-6016.
PDB code: 1nsj
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.