spacer
spacer

PDBsum entry 1jcm

Go to PDB code: 
protein ligands links
Lyase PDB id
1jcm
Jmol
Contents
Protein chain
259 a.a. *
Ligands
PO4 ×4
PO4-PO4
137
Waters ×135
* Residue conservation analysis
PDB id:
1jcm
Name: Lyase
Title: Trpc stability mutant containing an engineered disulphide br in complex with a cdrp-related substrate
Structure: Indole-3-glycerol-phosphate synthase. Chain: p. Fragment: n-terminal domain (1-259 aa) of the bifunctional anthranilate isomerase, igps:prai. Synonym: igps. Tryptophan biosynthesis protein trpcf. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Trimer (from PQS)
Resolution:
2.10Å     R-factor:   0.241     R-free:   0.319
Authors: A.Ivens,O.Mayans,H.Szadkowski,M.Wilmanns,K.Kirschner
Key ref:
A.Ivens et al. (2002). Stabilization of a (betaalpha)8-barrel protein by an engineered disulfide bridge. Eur J Biochem, 269, 1145-1153. PubMed id: 11856350 DOI: 10.1046/j.1432-1033.2002.02745.x
Date:
10-Jun-01     Release date:   10-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00909  (TRPC_ECOLI) -  Tryptophan biosynthesis protein TrpCF
Seq:
Struc:
453 a.a.
259 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: 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
Bound ligand (Het Group name = 137)
corresponds exactly
= 1-C- (3-indolyl)-glycerol 3-phosphate
+ CO(2)
+ H(2)O
   Enzyme class 2: E.C.5.3.1.24  - Phosphoribosylanthranilate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1- deoxy-D-ribulose 5-phosphate
N-(5-phospho-beta-D-ribosyl)anthranilate
Bound ligand (Het Group name = 137)
corresponds exactly
= 1-(2-carboxyphenylamino)-1- deoxy-D-ribulose 5-phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1046/j.1432-1033.2002.02745.x Eur J Biochem 269:1145-1153 (2002)
PubMed id: 11856350  
 
 
Stabilization of a (betaalpha)8-barrel protein by an engineered disulfide bridge.
A.Ivens, O.Mayans, H.Szadkowski, C.Jürgens, M.Wilmanns, K.Kirschner.
 
  ABSTRACT  
 
The aim of this study was to increase the stability of the thermolabile (betaalpha)8-barrel enzyme indoleglycerol phosphate synthase from Escherichia coli by the introduction of disulfide bridges. For the design of such variants, we selected two out of 12 candidates, in which newly introduced cysteines potentially form optimal disulfide bonds. These variants avoid short-range connections, substitutions near catalytic residues, and crosslinks between the new and the three parental cysteines. The variant linking residues 3 and 189 fastens the N-terminus to the (betaalpha)8-barrel. The rate of thermal inactivation at 50 degrees C of this variant with a closed disulfide bridge is 65-fold slower than that of the reference dithiol form, but only 13-fold slower than that of the parental protein. The near-ultraviolet CD spectrum, the reactivity of parental buried cysteines with Ellman's reagent as well as the decreased turnover number indicate that the protein structure is rigidified. To confirm these data, we have solved the X-ray structure to 2.1-A resolution. The second variant was designed to crosslink the terminal modules betaalpha1 and betaalpha8. However, not even the dithiol form acquired the native fold, possibly because one of the targeted residues is solvent-inaccessible in the parental protein.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Stereo representation of indoleglycerol phosphate synthase from E. coli . The bound phosphate ion indicates the location of the active site. The C positions of native cysteines (54, 113 and 134) and of the planned disulfide bonds (3–189) and (64–240) are shown. 15, position of the single tryptophan residue.
Figure 3.
Fig. 3. 2F[obs] -F [calc] / [calc] electron density map showing the disulfide bond contoured at 1.0 . The newly introduced cysteine residues C3 and C189 are labelled (black dots, Sulfur atoms).
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2002, 269, 1145-1153) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19533118 Z.L.Han, S.Y.Han, S.P.Zheng, and Y.Lin (2009).
Enhancing thermostability of a Rhizomucor miehei lipase by engineering a disulfide bond and displaying on the yeast cell surface.
  Appl Microbiol Biotechnol, 85, 117-126.  
16807887 J.L.Pellequer, and S.W.Chen (2006).
Multi-template approach to modeling engineered disulfide bonds.
  Proteins, 65, 192-202.  
16686937 O.R.Siadat, A.Lougarre, L.Lamouroux, C.Ladurantie, and D.Fournier (2006).
The effect of engineered disulfide bonds on the stability of Drosophila melanogaster acetylcholinesterase.
  BMC Biochem, 7, 12.  
15576565 J.J.Smith, D.W.Conrad, M.J.Cuneo, and H.W.Hellinga (2005).
Orthogonal site-specific protein modification by engineering reversible thiol protection mechanisms.
  Protein Sci, 14, 64-73.  
15645448 R.R.Thangudu, A.Vinayagam, G.Pugalenthi, A.Manonmani, B.Offmann, and R.Sowdhamini (2005).
Native and modeled disulfide bonds in proteins: knowledge-based approaches toward structure prediction of disulfide-rich polypeptides.
  Proteins, 58, 866-879.  
14681394 A.Vinayagam, G.Pugalenthi, R.Rajesh, and R.Sowdhamini (2004).
DSDBASE: a consortium of native and modelled disulphide bonds in proteins.
  Nucleic Acids Res, 32, D200-D202.  
15215524 R.Schultz-Heienbrok, T.Maier, and N.Sträter (2004).
Trapping a 96 degrees domain rotation in two distinct conformations by engineered disulfide bridges.
  Protein Sci, 13, 1811-1822.
PDB codes: 1oi8 1oid 1oie
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.