PDBsum entry 1dbf

Isomerase

PDB id: 1dbf

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

Protein chains

P19080  (AROH_BACSU) -  Chorismate mutase AroH from Bacillus subtilis (strain 168)

Seq: 127 a.a.

Struc: 127 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.5.4.99.5 - chorismate mutase.
• Pathway: Phenylalanine and Tyrosine Biosynthesis
• Reaction: chorismate = prephenate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

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 Å 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.