PDBsum entry 6dyt

Lyase

PDB id: 6dyt

Contents

Protein chains

455 a.a.

Ligands

F0G

PP3

P33

Metals

__K ×2

Waters ×623

PDB id:

6dyt

Name:

Lyase

Title:

Citrobacter freundii tyrosine phenol-lyase f448a mutant complexed with l-alanine

Structure:

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

Source:

Citrobacter freundii. Organism_taxid: 546. Atcc: 29063. Gene: tpl. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.05Å R-factor: 0.188 R-free: 0.232

Authors:

R.S.Phillips

Key ref:

R.S.Phillips and S.Craig (2018). Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism. Biochemistry, 57, 6166-6179. PubMed id: 30260636 DOI: 10.1021/acs.biochem.8b00724

Date:

02-Jul-18 Release date: 10-Oct-18

Protein chains

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

Seq: 456 a.a.

Struc: 455 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.1.99.2 - tyrosine phenol-lyase.
• Reaction: L-tyrosine + H2O = phenol + pyruvate + NH4⁺
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = F0G) matches with 68.18% similarity)

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

reference

DOI no: 10.1021/acs.biochem.8b00724

Biochemistry 57:6166-6179 (2018)

PubMed id: 30260636

Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism.

R.S.Phillips, S.Craig.

ABSTRACT

Tyrosine phenol-lyase (TPL; EC 4.1.99.2) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the reversible hydrolytic cleavage of l-tyrosine to phenol and ammonium pyruvate. We have shown previously that F448A TPL has k_cat and k_cat/ K_m values for l-tyrosine reduced by ∼10⁴-fold [Phillips, R. S., Vita, A., Spivey, J. B., Rudloff, A. P., Driscoll, M. D., and Hay, S. (2016) ACS Catal. 6, 6770-6779]. We have now obtained crystal structures of F448A TPL and complexes with l-alanine, l-methionine, l-phenylalanine, and 3-F-l-tyrosine at 2.05-2.27 Å and the complex of wild-type TPL with l-phenylalanine at 1.8 Å. The small domain of F448A TPL, where Phe-448 is located, is more disordered in chain A than in wild-type TPL. The complexes of F448A TPL with l-alanine and l-phenylalanine are in an open conformation in both chains, while the complex with l-methionine is a 52:48 open:closed equilibrium mixture in chain A. Wild-type TPL with l-alanine is closed in chain A and open in chain B, and the complex with l-phenylalanine is a 56:44 open:closed mixture in chain A. Thus, the Phe-448 to alanine mutation affects the conformational equilibrium of open and closed active sites. The structure of the 3-F-l-tyrosine quinonoid complex of F448A TPL is unstrained and in an open conformation, with a hydrogen bond from the phenolic OH to Thr-124. These results support our previous conclusion that ground-state strain plays a critical role in the mechanism of TPL.