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PDBsum entry 1dbf

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1dbf
Jmol
Contents
Protein chains
127 a.a. *
Ligands
SO4 ×9
GOL ×5
Waters ×424
* Residue conservation analysis
PDB id:
1dbf
Name: Isomerase
Title: Chorismate mutase from bacillus subtilis at 1.30 angstrom
Structure: Protein (chorismate mutase). Chain: a, b, c. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
1.30Å     R-factor:   0.169     R-free:   0.235
Authors: G.L.Gilliland,J.E.Ladner
Key ref:
J.E.Ladner et al. (2000). The 1.30 A resolution structure of the Bacillus subtilis chorismate mutase catalytic homotrimer. Acta Crystallogr D Biol Crystallogr, 56, 673-683. PubMed id: 10818343 DOI: 10.1107/S0907444900004625
Date:
02-Nov-99     Release date:   07-Jun-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19080  (AROH_BACSU) -  Chorismate mutase AroH
Seq:
Struc:
127 a.a.
127 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.5.4.99.5  - Chorismate mutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Phenylalanine and Tyrosine Biosynthesis
      Reaction: Chorismate = prephenate
Chorismate
= prephenate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     cellular amino acid biosynthetic process   3 terms 
  Biochemical function     isomerase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444900004625 Acta Crystallogr D Biol Crystallogr 56:673-683 (2000)
PubMed id: 10818343  
 
 
The 1.30 A resolution structure of the Bacillus subtilis chorismate mutase catalytic homotrimer.
J.E.Ladner, P.Reddy, A.Davis, M.Tordova, A.J.Howard, G.L.Gilliland.
 
  ABSTRACT  
 
The crystal structure of the Bacillus subtilis chorismate mutase, an enzyme of the aromatic amino acids biosynthetic pathway, was determined to 1.30 A resolution. The structure of the homotrimer was determined by molecular replacement using orthorhombic crystals of space group P2(1)2(1)2(1) with unit-cell parameters a = 52.2, b = 83. 8, c = 86.0 A. The ABC trimer of the was used as the starting model. The final coordinates are composed of three complete polypeptide chains of 127 amino-acid residues. In addition, there are nine sulfate ions, five glycerol molecules and 424 water molecules clearly visible in the structure. This structure was refined with aniosotropic temperature factors, has excellent geometry and a crystallographic R factor of 0.169 with an R(free) of 0.236. The three active sites of the macromolecule are at the subunit interfaces, with residues from two subunits contributing to each site. This orthorhombic crystal form was grown using ammonium sulfate as the precipitant; glycerol was used as a cryoprotectant during data collection. A glycerol molecule and sulfate ion in each of the active sites was found mimicking a transition-state analog. In this structure, the C-terminal tails of the subunits of the trimer are hydrogen bonded to residues of the active site of neighboring trimers in the crystal and thus cross-link the molecules in the crystal lattice.
 
  Selected figure(s)  
 
Figure 8.
Figure 8 Four examples of the double conformations included in the model. The A conformation is depicted with ball-and-stick models and the B conformation with only stick models. The electron density is contoured at 0.7 for chain A Met45, at 0.8 for chain B Glu40, at 2.0 for chain C Met76 and at 1.0 for chain A Val91.
Figure 9.
Figure 9 Portions of the C-terminal tails are shown with their electron density. Chain A is shown in pink and belongs to the primary molecule; chain B is shown in green and belongs to symmetry neighbor 14; chain C is shown in blue and belongs to symmetry neighbor 5. The electron density is contoured at 1 and for clarity is shown only within 2 of the included atoms. This figure was generated in TURBO-FRODO (Roussel et al., 1996[Roussel, A., Inisan, A.-G. & Cambillau, C. (1996). AFMB and Bio Graphics. Marseille, France.]).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 673-683) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21243152 F.Claeyssens, K.E.Ranaghan, N.Lawan, S.J.Macrae, F.R.Manby, J.N.Harvey, and A.J.Mulholland (2011).
Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions.
  Org Biomol Chem, 9, 1578-1590.  
17146044 S.K.Kim, S.K.Reddy, B.C.Nelson, G.B.Vasquez, A.Davis, A.J.Howard, S.Patterson, G.L.Gilliland, J.E.Ladner, and P.T.Reddy (2006).
Biochemical and structural characterization of the secreted chorismate mutase (Rv1885c) from Mycobacterium tuberculosis H37Rv: an *AroQ enzyme not regulated by the aromatic amino acids.
  J Bacteriol, 188, 8638-8648.
PDB code: 2f6l
11455603 D.T.Gallagher, M.Mayhew, M.J.Holden, A.Howard, K.J.Kim, and V.L.Vilker (2001).
The crystal structure of chorismate lyase shows a new fold and a tightly retained product.
  Proteins, 44, 304-311.
PDB codes: 1fw9 1g1b 1g81
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.