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PDBsum entry 2tpl

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
2tpl
Jmol
Contents
Protein chains
455 a.a. *
Ligands
HPP
Metals
_CS ×2
Waters ×252
* Residue conservation analysis
PDB id:
2tpl
Name: Lyase
Title: Tyrosine phenol-lyase from citrobacter intermedius complex w hydroxyphenyl)propionic acid, pyridoxal-5'-phosphate and cs
Structure: Tyrosine phenol-lyase. Chain: a, b. Ec: 4.1.99.2
Source: Citrobacter freundii. Organism_taxid: 546
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
2.50Å     R-factor:   0.183     R-free:   0.263
Authors: A.A.Antson,T.V.Demidkina,K.S.Wilson
Key ref: B.Sundararaju et al. (1997). The crystal structure of Citrobacter freundii tyrosine phenol-lyase complexed with 3-(4'-hydroxyphenyl)propionic acid, together with site-directed mutagenesis and kinetic analysis, demonstrates that arginine 381 is required for substrate specificity. Biochemistry, 36, 6502-6510. PubMed id: 9174368 DOI: 10.1021/bi962917+
Date:
23-Jan-97     Release date:   01-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P31013  (TPL_CITFR) -  Tyrosine phenol-lyase
Seq:
Struc:
456 a.a.
455 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.1.99.2  - Tyrosine phenol-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-tyrosine + H2O = phenol + pyruvate + NH3
L-tyrosine
Bound ligand (Het Group name = HPP)
matches with 92.31% similarity
+ H(2)O
= phenol
+ pyruvate
+ NH(3)
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellular amino acid metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi962917+ Biochemistry 36:6502-6510 (1997)
PubMed id: 9174368  
 
 
The crystal structure of Citrobacter freundii tyrosine phenol-lyase complexed with 3-(4'-hydroxyphenyl)propionic acid, together with site-directed mutagenesis and kinetic analysis, demonstrates that arginine 381 is required for substrate specificity.
B.Sundararaju, A.A.Antson, R.S.Phillips, T.V.Demidkina, M.V.Barbolina, P.Gollnick, G.G.Dodson, K.S.Wilson.
 
  ABSTRACT  
 
The X-ray structure of tyrosine phenol-lyase (TPL) complexed with a substrate analog, 3-(4'-hydroxyphenyl)propionic acid, shows that Arg 381 is located in the substrate binding site, with the side-chain NH1 4.1 A from the 4'-OH of the analog. The structure has been deduced at 2.5 A resolution using crystals that belong to the P2(1)2(1)2 space group with a = 135.07 A, b = 143.91 A, and c = 59.80 A. To evaluate the role of Arg 381 in TPL catalysis, we prepared mutant proteins replacing arginine with alanine (R381A), with isoleucine (R381I), and with valine (R381V). The beta-elimination activity of R381A TPL has been reduced by 10(-4)-fold compared to wild type, whereas R381I and R381V TPL exhibit no detectable beta-elimination activity with L-tyrosine as substrate. However, R381A, R381I, and R381V TPL react with S-(o-nitrophenyl)-L-cysteine, beta-chloro-L-alanine, O-benzoyl-L-serine, and S-methyl-L-cysteine and exhibit k(cat) and k(cat)/Km values comparable to those of wild-type TPL. Furthermore, the Ki values for competitive inhibition by L-tryptophan and L-phenylalanine are similar for wild-type, R381A, and R381I TPL. Rapid-scanning-stopped flow spectroscopic analyses also show that wild-type and mutant proteins can bind L-tyrosine and form quinonoid complexes with similar rate constants. The binding of 3-(4'-hydroxyphenyl)propionic acid to wild-type TPL decreases at high pH values with a pKa of 8.4 and is thus dependent on an acidic group, possibly Arg404, which forms an ion pair with the analog carboxylate, or the pyridoxal 5'-phosphate Schiff base. R381A TPL shows only a small decrease in k(cat)/Km for tyrosine at lower pH, in contrast to wild-type TPL, which shows two basic pKas with an average value of about 7.8. Thus, it is possible that Arg 381 is one of the catalytic bases previously observed in the pH dependence of k(cat)/Km of TPL with L-tyrosine [Kiick, D. M., & Phillips. R. S. (1988) Biochemistry 27, 7333-7338], and hence Arg 381 is at least partially responsible for the substrate specificity of TPL.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19780833 E.Rha, S.Kim, S.L.Choi, S.P.Hong, M.H.Sung, J.J.Song, and S.G.Lee (2009).
Simultaneous improvement of catalytic activity and thermal stability of tyrosine phenol-lyase by directed evolution.
  FEBS J, 276, 6187-6194.  
18715865 D.Milić, T.V.Demidkina, N.G.Faleev, D.Matković-Calogović, and A.A.Antson (2008).
Insights into the catalytic mechanism of tyrosine phenol-lyase from X-ray structures of quinonoid intermediates.
  J Biol Chem, 283, 29206-29214.
PDB codes: 2vlf 2vlh
17766369 F.N.Musayev, M.L.di Salvo, T.P.Ko, A.K.Gandhi, A.Goswami, V.Schirch, and M.K.Safo (2007).
Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.
  Protein Sci, 16, 2184-2194.
PDB codes: 2yxt 2yxu
16768450 D.Milić, D.Matković-Calogović, T.V.Demidkina, V.V.Kulikova, N.I.Sinitzina, and A.A.Antson (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.
PDB codes: 2ez1 2ez2
16267046 E.Di Cera (2006).
A structural perspective on enzymes activated by monovalent cations.
  J Biol Chem, 281, 1305-1308.  
17094783 S.G.Lee, S.P.Hong, d.o. .Y.Kim, J.J.Song, H.S.Ro, and M.H.Sung (2006).
Inactivation of tyrosine phenol-lyase by Pictet-Spengler reaction and alleviation by T15A mutation on intertwined N-terminal arm.
  FEBS J, 273, 5564-5573.  
15044726 B.Pioselli, S.Bettati, T.V.Demidkina, L.N.Zakomirdina, R.S.Phillips, and A.Mozzarelli (2004).
Tyrosine phenol-lyase and tryptophan indole-lyase encapsulated in wet nanoporous silica gels: Selective stabilization of tertiary conformations.
  Protein Sci, 13, 913-924.  
15560798 N.G.Faleev, T.V.Demidkina, M.A.Tsvetikova, R.S.Phillips, and I.A.Yamskov (2004).
The mechanism of alpha-proton isotope exchange in amino acids catalysed by tyrosine phenol-lyase. What is the role of quinonoid intermediates?
  Eur J Biochem, 271, 4565-4571.  
14596599 T.Yamada, J.Komoto, Y.Takata, H.Ogawa, H.C.Pitot, and F.Takusagawa (2003).
Crystal structure of serine dehydratase from rat liver.
  Biochemistry, 42, 12854-12865.
PDB codes: 1pwe 1pwh
11900544 R.S.Phillips, N.Johnson, and A.V.Kamath (2002).
Formation in vitro of hybrid dimers of H463F and Y74F mutant Escherichia coli tryptophan indole-lyase rescues activity with L-tryptophan.
  Biochemistry, 41, 4012-4019.  
11934889 R.S.Phillips, T.V.Demidkina, L.N.Zakomirdina, S.Bruno, L.Ronda, and A.Mozzarelli (2002).
Crystals of tryptophan indole-lyase and tyrosine phenol-lyase form stable quinonoid complexes.
  J Biol Chem, 277, 21592-21597.  
10913261 B.Sundararaju, H.Chen, S.Shilcutt, and R.S.Phillips (2000).
The role of glutamic acid-69 in the activation of Citrobacter freundii tyrosine phenol-lyase by monovalent cations.
  Biochemistry, 39, 8546-8555.  
11114510 H.Erlandsen, E.E.Abola, and R.C.Stevens (2000).
Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites.
  Curr Opin Struct Biol, 10, 719-730.  
11082202 N.G.Faleev, Y.N.Zhukov, E.N.Khurs, O.I.Gogoleva, M.V.Barbolina, N.P.Bazhulina, V.M.Belikov, T.V.Demidkina, and R.M.Khomutov (2000).
Interaction of tyrosine phenol-lyase with phosphoroorganic analogues of substrate amino acids.
  Eur J Biochem, 267, 6897-6902.  
10079072 A.A.Morollo, G.A.Petsko, and D.Ringe (1999).
Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase.
  Biochemistry, 38, 3293-3301.
PDB code: 2sfp
9880502 B.Mouratou, P.Kasper, H.Gehring, and P.Christen (1999).
Conversion of tyrosine phenol-lyase to dicarboxylic amino acid beta-lyase, an enzyme not found in nature.
  J Biol Chem, 274, 1320-1325.  
10328314 K.Kim, and P.A.Cole (1999).
Synthesis of (2S,3R)-beta-methyltyrosine catalyzed by tyrosine phenol-lyase.
  Bioorg Med Chem Lett, 9, 1205-1208.  
10373003 K.Pawłowski, B.Zhang, L.Rychlewski, and A.Godzik (1999).
The Helicobacter pylori genome: from sequence analysis to structural and functional predictions.
  Proteins, 36, 20-30.  
9914259 J.N.Jansonius (1998).
Structure, evolution and action of vitamin B6-dependent enzymes.
  Curr Opin Struct Biol, 8, 759-769.  
9565551 K.H.Jhee, L.H.Yang, S.A.Ahmed, P.McPhie, R.Rowlett, and E.W.Miles (1998).
Mutation of an active site residue of tryptophan synthase (beta-serine 377) alters cofactor chemistry.
  J Biol Chem, 273, 11417-11422.  
9354624 H.Hayashi, and H.Kagamiyama (1997).
Transient-state kinetics of the reaction of aspartate aminotransferase with aspartate at low pH reveals dual routes in the enzyme-substrate association process.
  Biochemistry, 36, 13558-13569.  
9119037 R.S.Phillips, R.L.Von Tersch, and F.Secundo (1997).
Effects of tyrosine ring fluorination on rates and equilibria of formation of intermediates in the reactions of carbon-carbon lyases.
  Eur J Biochem, 244, 658-663.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.