Three-dimensional structure of tyrosine phenol-lyase

Biochemistry. 1993 Apr 27;32(16):4195-206. doi: 10.1021/bi00067a006.

Abstract

Tyrosine phenol-lyase (EC 4.1.99.2) from Citrobacter freundii has been cloned and the primary sequence deduced from the DNA sequence. From the BrCN digest of the NaBH4-reduced holoenzyme, five peptides were purified and sequenced. The amino acid sequences of the peptides agreed with the corresponding parts of the tyrosine phenol-lyase sequence obtained from the gene structure. K257 is the pyridoxal 5'-phosphate binding residue. Assisted by the sequence data, the crystal structure of apotyrosine phenol-lyase, a pyridoxal 5'-phosphate-dependent enzyme, has been refined to an R-factor of 16.2% at 2.3-A resolution using synchrotron radiation diffraction data. The tetrameric molecule has 222 symmetry, with one of the axes coincident with the crystallographic 2-fold symmetry axis of the crystal which belongs to the space group P2(1)2(1)2 with a = 76.0 A, b = 138.3 A, and c = 93.5 A. Each subunit comprises 14 alpha-helices and 16 beta-strands, which fold into a small and a large domain. The coenzyme-binding lysine residue is located at the interface between the large and small domains of one subunit and the large domain of a crystallographically related subunit. The fold of the large, pyridoxal 5'-phosphate binding domain and the location of the active site are similar to that found in aminotransferases. Most of the residues which participate in binding of pyridoxal 5'-phosphate in aminotransferases are conserved in the structure of tyrosine phenol-lyase. Two dimers of tyrosine phenol-lyase, each of which has a domain architecture similar to that found in aspartate aminotransferases, are bound together through a hydrophobic cluster in the center of the molecule and intertwined N-terminal arms.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Apoenzymes / chemistry
  • Base Sequence
  • Binding Sites
  • Citrobacter / enzymology
  • Citrobacter freundii / enzymology*
  • Citrobacter freundii / genetics
  • Cloning, Molecular
  • Genes, Bacterial
  • Genomic Library
  • Macromolecular Substances
  • Models, Molecular
  • Models, Structural
  • Molecular Sequence Data
  • Peptide Fragments / chemistry
  • Protein Structure, Secondary*
  • Recombinant Proteins / chemistry
  • Sequence Homology, Amino Acid
  • Tyrosine Phenol-Lyase / chemistry*
  • Tyrosine Phenol-Lyase / genetics*

Substances

  • Apoenzymes
  • Macromolecular Substances
  • Peptide Fragments
  • Recombinant Proteins
  • Tyrosine Phenol-Lyase

Associated data

  • GENBANK/L10821
  • GENBANK/L11865
  • GENBANK/L11866
  • GENBANK/L11867
  • GENBANK/L12214
  • GENBANK/L16873
  • GENBANK/L16874
  • GENBANK/L16875
  • GENBANK/L16876
  • GENBANK/L16878