PDBsum entry 1lc8

Lyase

PDB id: 1lc8

Contents

Protein chain

356 a.a. *

Ligands

33P

Waters ×271

* Residue conservation analysis

PDB id:

1lc8

Name:

Lyase

Title:

Crystal structure of l-threonine-o-3-phosphate decarboxylase from s. Enterica complexed with its reaction intermediate

Structure:

L-threonine-o-3-phosphate decarboxylase. Chain: a. Synonym: cobd. Engineered: yes

Source:

Salmonella enterica. Organism_taxid: 28901. Gene: cobd. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.80Å R-factor: 0.196 R-free: 0.229

Authors:

C.-G.Cheong,J.Escalante-Semerena,I.Rayment

Key ref:

C.G.Cheong et al. (2002). Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes. Biochemistry, 41, 9079-9089. PubMed id: 12119022 DOI: 10.1021/bi020294w

Date:

05-Apr-02 Release date: 28-Jun-02

Protein chain

P97084  (COBD_SALTY) -  Threonine-phosphate decarboxylase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: 364 a.a.

Struc: 356 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.4.1.1.81 - threonine-phosphate decarboxylase.
• Pathway: Corrin Biosynthesis (part 6)
• Reaction: O-phospho-L-threonine + H⁺ = (R)-1-aminopropan-2-yl phosphate + CO2
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = 33P) matches with 60.00% similarity)

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

reference

DOI no: 10.1021/bi020294w

Biochemistry 41:9079-9089 (2002)

PubMed id: 12119022

Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes.

C.G.Cheong, J.C.Escalante-Semerena, I.Rayment.

ABSTRACT

The evolution of biosynthetic pathways is difficult to reconstruct in hindsight; however, the structures of the enzymes that are involved may provide insight into their development. One enzyme in the cobalamin biosynthetic pathway that appears to have evolved from a protein with different function is L-threonine-O-3-phosphate decarboxylase (CobD) from Salmonella enterica, which is structurally similar to histidinol phosphate aminotransferase [Cheong, C. G., Bauer, C. B., Brushaber, K. R., Escalante-Semerena, J. C., and Rayment, I. (2002) Biochemistry 41, 4798-4808]. This enzyme is responsible for synthesizing (R)-1-amino-2-propanol phosphate which is the precursor for the linkage between the nucleotide loop and the corrin ring in cobalamin. To understand the relationship between this decarboxylase and the aspartate aminotransferase family to which it belongs, the structures of CobD in its apo state, the apo state complexed with the substrate, and its product external aldimine complex have been determined at 1.46, 1.8, and 1.8 A resolution, respectively. These structures show that the enzyme steers the breakdown of the external aldimine toward decarboxylation instead of amino transfer by positioning the carboxylate moiety of the substrate out of the plane of the pyridoxal ring and by placing the alpha-hydrogen out of reach of the catalytic base provided by the lysine that forms the internal aldimine. It would appear that CobD evolved from a primordial PLP-dependent aminotransferase, where the selection was based on similarities between the stereochemical properties of the substrates rather than preservation of the fate of the external aldimine. These structures provide a sequence signature for distinguishing between L-threonine-O-3-phosphate decarboxylase and histidinol phosphate aminotransferases, many of which appear to have been misannotated.