2VLF

Quinonoid intermediate of Citrobacter freundii tyrosine phenol-lyase formed with alanine

Summary for 2VLF

• Entry DOI: 10.2210/pdb2vlf/pdb
• Related: 1TPL 2EZ1 2EZ2 2TPL 2VLH
• Descriptor: TYROSINE PHENOL-LYASE, (2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}PROPANOIC ACID, TRIETHYLENE GLYCOL, ... (6 entities in total)
• Functional Keywords: plp-dependent enzyme, lyase, tyrosine degradation
• Biological source: CITROBACTER FREUNDII
• Total number of polymer chains: 2
• Total formula weight: 104324.76

Authors

Milic, D.,Demidkina, T.V.,Matkovic-Calogovic, D.,Antson, A.A. (deposition date: 2008-01-14, release date: 2008-08-19, Last modification date: 2023-12-13)

Primary citation

Milic, D.,Demidkina, T.V.,Faleev, N.G.,Matkovic-Calogovic, D.,Antson, A.A.
Insights Into the Catalytic Mechanism of Tyrosine Phenol-Lyase from X-Ray Structures of Quinonoid Intermediates.
J.Biol.Chem., 283:29206-, 2008

PubMed 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.

PubMed: 18715865
DOI: 10.1074/JBC.M802061200

Experimental method

X-RAY DIFFRACTION (1.89 Å)