PDBsum entry 2ez2

Lyase

PDB id: 2ez2

Contents

Protein chains

456 a.a. *

Ligands

PO4 ×2

Metals

__K ×2

Waters ×1021

* Residue conservation analysis

PDB id:

2ez2

Name:

Lyase

Title:

Apo tyrosine phenol-lyase from citrobacter freundii at ph 8.0

Structure:

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

Source:

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

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.85Å R-factor: 0.175 R-free: 0.206

Authors:

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

Key ref:

D.Milić et al. (2006). Structures of apo- and holo-tyrosine phenol-lyase reveal a catalytically critical closed conformation and suggest a mechanism for activation by K+ ions. Biochemistry, 45, 7544-7552. PubMed id: 16768450 DOI: 10.1021/bi0601858

Date:

10-Nov-05 Release date: 25-Jul-06

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⁺
• Cofactor: Pyridoxal 5'-phosphate

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

reference

DOI no: 10.1021/bi0601858

Biochemistry 45:7544-7552 (2006)

PubMed id: 16768450

Structures of apo- and holo-tyrosine phenol-lyase reveal a catalytically critical closed conformation and suggest a mechanism for activation by K+ ions.

D.Milić, D.Matković-Calogović, T.V.Demidkina, V.V.Kulikova, N.I.Sinitzina, A.A.Antson.

ABSTRACT

Tyrosine phenol-lyase, a tetrameric pyridoxal 5'-phosphate dependent enzyme, catalyzes the reversible hydrolytic cleavage of L-tyrosine to phenol and ammonium pyruvate. Here we describe the crystal structure of the Citrobacter freundii holoenzyme at 1.9 A resolution. The structure reveals a network of protein interactions with the cofactor, pyridoxal 5'-phosphate, and details of coordination of the catalytically important K+ ion. We also present the structure of the apoenzyme at 1.85 A resolution. Both structures were determined using crystals grown at pH 8.0, which is close to the pH of the maximal enzymatic activity (8.2). Comparison of the apoenzyme structure with the one previously determined at pH 6.0 reveals significant differences. The data suggest that the decrease of the enzymatic activity at pH 6.0 may be caused by conformational changes in the active site residues Tyr71, Tyr291, and Arg381 and in the monovalent cation binding residue Glu69. Moreover, at pH 8.0 we observe two different active site conformations: open, which was characterized before, and closed, which is observed for the first time in beta-eliminating lyases. In the closed conformation a significant part of the small domain undergoes an extraordinary motion of up to 12 A toward the large domain, closing the active site cleft and bringing the catalytically important Arg381 and Phe448 into the active site. The closed conformation allows rationalization of the results of previous mutational studies and suggests that the observed active site closure is critical for the course of the enzymatic reaction and for the enzyme's specificity toward its physiological substrate. Finally, the closed conformation allows us to model keto(imino)quinonoid, the key transition intermediate.