1TPL

THE THREE-DIMENSIONAL STRUCTURE OF TYROSINE PHENOL-LYASE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Three-dimensional structure of tyrosine phenol-lyase.

Antson, A.A., Demidkina, T.V., Gollnick, P., Dauter, Z., von Tersch, R.L., Long, J., Berezhnoy, S.N., Phillips, R.S., Harutyunyan, E.H., Wilson, K.S.

(1993) Biochemistry 32: 4195-4206

  • DOI: 10.1021/bi00067a006
  • Primary Citation of Related Structures:  
    1TPL

  • PubMed 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 ...

    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.

    Related Citations: 
    • The Polypeptide Chain Fold in Tyrosine Phenol-Lyase, a Pyridoxal-5'-Phosphate-Dependent Enzyme
      Antson, A.A., Strokopytov, B.V., Murshudov, G.N., Isupov, M.N., Harutyunyan, E.H., Demidkina, T.V., Vassylyev, D.G., Dauter, Z., Terry, H., Wilson, K.S.
      (1992) FEBS Lett 302: 256
    Organizational Affiliation: 

    Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TYROSINE PHENOL-LYASEA, B456Citrobacter intermediusMutation(s): 0 
EC: 4.1.99.2
UniProt
Find proteins for P31013 (Citrobacter freundii)
Explore P31013 
Go to UniProtKB:  P31013
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31013
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.02α = 90
b = 138.27β = 90
c = 93.54γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model