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PDBsum entry 1i4n

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1i4n
Jmol
Contents
Protein chains
251 a.a. *
Ligands
SO4 ×2
Waters ×80
* Residue conservation analysis
PDB id:
1i4n
Name: Lyase
Title: Crystal structure of indoleglycerol phosphate synthase from thermotoga maritima
Structure: Indole-3-glycerol phosphate synthase. Chain: a, b. Synonym: indoleglycerol phosphate synthase, igps. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.50Å     R-factor:   0.169     R-free:   0.233
Authors: T.Knoechel,A.Pappenberger,J.N.Jansonius,K.Kirschner
Key ref:
T.Knöchel et al. (2002). The crystal structure of indoleglycerol-phosphate synthase from Thermotoga maritima. Kinetic stabilization by salt bridges. J Biol Chem, 277, 8626-8634. PubMed id: 11741953 DOI: 10.1074/jbc.M109517200
Date:
22-Feb-01     Release date:   20-Mar-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q56319  (TRPC_THEMA) -  Indole-3-glycerol phosphate synthase
Seq:
Struc:
252 a.a.
251 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: 10.1074/jbc.M109517200 J Biol Chem 277:8626-8634 (2002)
PubMed id: 11741953  
 
 
The crystal structure of indoleglycerol-phosphate synthase from Thermotoga maritima. Kinetic stabilization by salt bridges.
T.Knöchel, A.Pappenberger, J.N.Jansonius, K.Kirschner.
 
  ABSTRACT  
 
The crystal structure of the thermostable indoleglycerol-phosphate synthase from Thermotoga maritima (tIGPS) was determined at 2.5 A resolution. It was compared with the structures of the thermostable sIGPS from Sulfolobus solfataricus and of the thermolabile eIGPS from Escherichia coli. The main chains of the three (beta alpha)(8)-barrel proteins superimpose closely, and the packing of side chains in the beta-barrel cores, as well as the architecture of surface loops, is very similar. Both thermostable proteins have, however, 17 strong salt bridges, compared with only 10 in eIGPS. The number of additional salt bridges in tIGPS and sIGPS correlates well with their reduced rate of irreversible thermal inactivation at 90 degrees C. Only 3 of 17 salt bridges in tIGPS and sIGPS are topologically conserved. The major difference between the two proteins is the preference for interhelical salt bridges in sIGPS and intrahelical ones in tIGPS. The different implementation of salt bridges in the closely related proteins suggests that the stabilizing effect of salt bridges depends rather on the sum of their individual contributions than on their location. This observation is consistent with a protein unfolding mechanism where the simultaneous breakdown of all salt bridges is the rate-determining step.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. a, disulfide-linked dimer of tIGPS viewed down the non-crystallographic rotation axis. Molecule A ( top) is shown in green and molecule B (bottom) in cyan. N and C termini are labeled. The angle for rotating molecule B onto molecule A is = 194.6°. The side chains of Cys102 and the sulfate ions (labeled S) are depicted as ball-and-stick models. b, stereo view of the enlarged interface region framed in a, with the same view direction. The structural model is superimposed on the 2F[o] F[c] electron density map contoured at 1.0 . c, superimposed C traces of tIGPS (black), sIGPS (red), and eIGPS (blue), viewed with the barrel axis vertical in the plane of the figure. In the C trace of tIGPS the N- and C-terminal residues are labeled, and every 10th residue is highlighted by a dot, and every 50th residue is numbered. Drawings were produced with MOLSCRIPT (56) and QUANTA (Version 98.1111; Accelrys Inc., San Diego, CA).
Figure 4.
Fig. 4. Ball-and-stick models, in stereo, of loop [2] [2] in molecule A of tIGPS (a) and in eIGPS (b). Hydrogen bonds between the main chain amide protons and the negatively charged side chains Glu83 in tIGPS or Asp89 in eIGPS are shown as broken lines. The respective distances (Å) are also given. Drawings were produced with MOLSCRIPT (56).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 8626-8634) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
15598351 S.Cheek, Y.Qi, S.S.Krishna, L.N.Kinch, and N.V.Grishin (2004).
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies.
  BMC Bioinformatics, 5, 197.  
12381840 O.Bogin, I.Levin, Y.Hacham, S.Tel-Or, M.Peretz, F.Frolow, and Y.Burstein (2002).
Structural basis for the enhanced thermal stability of alcohol dehydrogenase mutants from the mesophilic bacterium Clostridium beijerinckii: contribution of salt bridging.
  Protein Sci, 11, 2561-2574.
PDB code: 1jqb
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