PDBsum entry 1v7c

Lyase

PDB id: 1v7c

Contents

Protein chains

351 a.a. *

Ligands

HEY ×4

Waters ×885

* Residue conservation analysis

PDB id:

1v7c

Name:

Lyase

Title:

Crystal structure of threonine synthase from thermus thermophilus hb8 in complex with a substrate analogue

Structure:

Threonine synthase. Chain: a, b, c, d. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Gene: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.196 R-free: 0.230

Authors:

R.Omi,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

R.Omi et al. (2003). Crystal structures of threonine synthase from Thermus thermophilus HB8: conformational change, substrate recognition, and mechanism. J Biol Chem, 278, 46035-46045. PubMed id: 12952961 DOI: 10.1074/jbc.M308065200

Date:

16-Dec-03 Release date: 30-Dec-03

Supersedes:

1uiq

Protein chains

P83823  (P83823_THETH) -  Threonine synthase from Thermus thermophilus

Seq: 351 a.a.

Struc: 351 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.3.1 - threonine synthase.
• Pathway: Threonine Biosynthesis
• Reaction: O-phospho-L-homoserine + H2O = L-threonine + phosphate
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = HEY) matches with 53.57% similarity)

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

reference

DOI no: 10.1074/jbc.M308065200

J Biol Chem 278:46035-46045 (2003)

PubMed id: 12952961

Crystal structures of threonine synthase from Thermus thermophilus HB8: conformational change, substrate recognition, and mechanism.

R.Omi, M.Goto, I.Miyahara, H.Mizuguchi, H.Hayashi, H.Kagamiyama, K.Hirotsu.

ABSTRACT

Threonine synthase, which is a PLP-dependent enzyme, catalyzes the beta,gamma-replacement reaction of l-homoserine phosphate to yield threonine and inorganic phosphate. The three-dimensional structures of the enzyme from Thermus thermophilus HB8 in its unliganded form and complexed with the substrate analogue 2-amino-5-phosphonopentanoic acid have been determined at 2.15 and 2.0 A resolution, respectively. The complexed form, assigned as an enamine, uncovered the interactions of the cofactor-analogue conjugate with the active site residues. The binding of the substrate analogue induces a large conformational change at the domain level. The small domain rotates by about 25 degrees and approaches the large domain to close the active site. The complicated catalytic process of the enzyme has been elucidated based on the complex structure to reveal the stereochemistry of the reaction and to present the released inorganic phosphate as a possible catalyst to carry a proton to the Cgamma atom of the substrate.

Selected figure(s)

Figure 6.
FIG. 6. Schematic diagram showing hydrogen bond and salt bridge interactions of the active site residues. The unliganded tThrS (A) and tThrS·AP5 complex (B). Putative interactions are shown by dotted lines if the acceptor and donor are less than 3.3 Å apart.

Figure 9.
FIG. 9. The proposed reaction mechanism of ThrS with the substrate, HSerP. A, Michaelis complex; B, external aldimine; C, carbanion intermediate; D, ketimine; E, enamine; F, , -unsaturated ketimine; G, , -unsaturated aldimine; H, external aldimine between PLP and threonine.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 46035-46045) copyright 2003.

Figures were selected by an automated process.