PDBsum entry 2vlh

Lyase

PDB id: 2vlh

Contents

Protein chains

456 a.a. *

Ligands

PM9

PGE

P33

PLP

Metals

__K ×2

Waters ×887

* Residue conservation analysis

PDB id:

2vlh

Name:

Lyase

Title:

Quinonoid intermediate of citrobacter freundii tyrosine phenol-lyase formed with methionine

Structure:

Tyrosine phenol-lyase. Chain: a, b. Synonym: beta-tyrosinase. Engineered: yes

Source:

Citrobacter freundii. Organism_taxid: 546. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.95Å R-factor: 0.156 R-free: 0.192

Authors:

D.Milic,T.V.Demidkina,D.Matkovic-Calogovic,A.A.Antson

Key ref:

D.Milić et al. (2008). Insights into the catalytic mechanism of tyrosine phenol-lyase from X-ray structures of quinonoid intermediates. J Biol Chem, 283, 29206-29214. PubMed id: 18715865 DOI: 10.1074/jbc.M802061200

Date:

14-Jan-08 Release date: 19-Aug-08

Protein chains

P31013  (TPL_CITFR) -  Tyrosine phenol-lyase from Citrobacter freundii

Seq: 456 a.a.

Struc: 456 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.99.2 - tyrosine phenol-lyase.
• Reaction: L-tyrosine + H2O = phenol + pyruvate + NH4⁺

L-tyrosine + H2O = phenol + pyruvate (Bound ligand (Het Group name = PLP) matches with 46.67% similarity) + NH4(+)

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PM9) matches with 60.00% similarity)

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

reference

DOI no: 10.1074/jbc.M802061200

J Biol Chem 283:29206-29214 (2008)

PubMed id: 18715865

Insights into the catalytic mechanism of tyrosine phenol-lyase from X-ray structures of quinonoid intermediates.

D.Milić, T.V.Demidkina, N.G.Faleev, D.Matković-Calogović, A.A.Antson.

ABSTRACT

Amino acid transformations catalyzed by a number of pyridoxal 5'-phosphate (PLP)-dependent enzymes involve abstraction of the Calpha proton from an external aldimine formed between a substrate and the cofactor leading to the formation of a quinonoid intermediate. Despite the key role played by the quinonoid intermediates in the catalysis by PLP-dependent enzymes, limited accurate information is available about their structures. We trapped the quinonoid intermediates of Citrobacter freundii tyrosine phenol-lyase with L-alanine and L-methionine in the crystalline state and determined their structures at 1.9- and 1.95-A resolution, respectively, by cryo-crystallography. The data reveal a network of protein-PLP-substrate interactions that stabilize the planar geometry of the quinonoid intermediate. In both structures the protein subunits are found in two conformations, open and closed, uncovering the mechanism by which binding of the substrate and restructuring of the active site during its closure protect the quinonoid intermediate from the solvent and bring catalytically important residues into positions suitable for the abstraction of phenol during the beta-elimination of L-tyrosine. In addition, the structural data indicate a mechanism for alanine racemization involving two bases, Lys-257 and a water molecule. These two bases are connected by a hydrogen bonding system allowing internal transfer of the Calpha proton.

Selected figure(s)

Figure 1.
TPL tetramer. Ribbon diagram with different subunits shown in different colors. One catalytic dimer consists of the subunits shown in cyan and blue, while the other is formed from the subunits shown in orange and yellow. PLP and the side chains of the PLP-binding Lys-257 residues are shown as spheres. The view is along the crystallographic 2-fold axis.

Figure 3.
Enzyme interactions with the Ala quinonoid intermediate in the closed (A) and open (B) active sites. Stereo views with structures of quinonoid and two water molecules superposed with the corresponding weighted |F[o]| - |F[c]| electron density omit maps (green) are contoured at the 3.0σ level. Hydrogen bonds are denoted by dashed lines. Carbon atoms of residues belonging to the large rigid region are shown in orange, those from the small rigid region are shown in pink, and the residues from the neighboring subunit are shown in blue and labeled with a star. The alternate conformations of Thr-124, Thr-216, Met-288, and Phe-449 in the open conformation are shown in corresponding pale tones.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 29206-29214) copyright 2008.

Figures were selected by an automated process.