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PDBsum entry 1w27

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1w27
Jmol
Contents
Protein chains
690 a.a. *
Ligands
DTT ×2
Waters ×1071
* Residue conservation analysis
PDB id:
1w27
Name: Lyase
Title: Phenylalanine ammonia-lyase (pal) from petroselinum crispum
Structure: Phenylalanine ammonia-lyase 1. Chain: a, b. Engineered: yes
Source: Petroselinum crispum. Parsley. Organism_taxid: 4043. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: synthetic gene
Biol. unit: Tetramer (from PDB file)
Resolution:
1.70Å     R-factor:   0.168     R-free:   0.199
Authors: H.Ritter,G.E.Schulz
Key ref: H.Ritter and G.E.Schulz (2004). Structural basis for the entrance into the phenylpropanoid metabolism catalyzed by phenylalanine ammonia-lyase. Plant Cell, 16, 3426-3436. PubMed id: 15548745 DOI: 10.1105/tpc.104.025288
Date:
29-Jun-04     Release date:   25-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P24481  (PAL1_PETCR) -  Phenylalanine ammonia-lyase 1
Seq:
Struc:
 
Seq:
Struc:
716 a.a.
690 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.3.1.24  - Phenylalanine ammonia-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-phenylalanine = trans-cinnamate + ammonia
L-phenylalanine
= trans-cinnamate
+ ammonia
      Cofactor: MIO
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     biosynthetic process   4 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1105/tpc.104.025288 Plant Cell 16:3426-3436 (2004)
PubMed id: 15548745  
 
 
Structural basis for the entrance into the phenylpropanoid metabolism catalyzed by phenylalanine ammonia-lyase.
H.Ritter, G.E.Schulz.
 
  ABSTRACT  
 
Because of its key role in secondary phenylpropanoid metabolism, Phe ammonia-lyase is one of the most extensively studied plant enzymes. To provide a basis for detailed structure-function studies, the enzyme from parsley (Petroselinum crispum) was crystallized, and the structure was elucidated at 1.7-A resolution. It contains the unusual electrophilic 4-methylidene-imidazole-5-one group, which is derived from a tripeptide segment in two autocatalytic dehydration reactions. The enzyme resembles His ammonia-lyase from the general His degradation pathway but contains 207 additional residues, mainly in an N-terminal extension rigidifying a domain interface and in an inserted alpha-helical domain restricting the access to the active center. Presumably, Phe ammonia-lyase developed from His ammonia-lyase when fungi and plants diverged from the other kingdoms. A pathway of the catalyzed reaction is proposed in agreement with established biochemical data. The inactivation of the enzyme by a nucleophile is described in detail.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20354908 L.S.Hsieh, Y.L.Hsieh, C.S.Yeh, C.Y.Cheng, C.C.Yang, and P.D.Lee (2011).
Molecular characterization of a phenylalanine ammonia-lyase gene (BoPAL1) from Bambusa oldhamii.
  Mol Biol Rep, 38, 283-290.  
21131229 N.J.Turner (2011).
Ammonia lyases and aminomutases as biocatalysts for the synthesis of α-amino and β-amino acids.
  Curr Opin Chem Biol, 15, 234-240.  
21052759 X.Wang (2011).
Structure, function, and engineering of enzymes in isoflavonoid biosynthesis.
  Funct Integr Genomics, 11, 13-22.  
20924508 B.Wu, W.Szymański, H.J.Wijma, C.G.Crismaru, S.de Wildeman, G.J.Poelarends, B.L.Feringa, and D.B.Janssen (2010).
Engineering of an enantioselective tyrosine aminomutase by mutation of a single active site residue in phenylalanine aminomutase.
  Chem Commun (Camb), 46, 8157-8159.  
20563822 C.Weitzel, and M.Petersen (2010).
Enzymes of phenylpropanoid metabolism in the important medicinal plant Melissa officinalis L.
  Planta, 232, 731-742.  
20642725 J.K.Weng, and C.Chapple (2010).
The origin and evolution of lignin biosynthesis.
  New Phytol, 187, 273-285.  
20693685 M.Li, A.Gustchina, F.S.Rasulova, E.E.Melnikov, M.R.Maurizi, T.V.Rotanova, Z.Dauter, and A.Wlodawer (2010).
Structure of the N-terminal fragment of Escherichia coli Lon protease.
  Acta Crystallogr D Biol Crystallogr, 66, 865-873.
PDB code: 3ljc
21036782 S.Bartsch, and U.T.Bornscheuer (2010).
Mutational analysis of phenylalanine ammonia lyase to improve reactions rates for various substrates.
  Protein Eng Des Sel, 23, 929-933.  
20035037 T.Vogt (2010).
Phenylpropanoid biosynthesis.
  Mol Plant, 3, 2.  
19123196 B.Wu, W.Szymanski, P.Wietzes, S.de Wildeman, G.J.Poelarends, B.L.Feringa, and D.B.Janssen (2009).
Enzymatic Synthesis of Enantiopure alpha- and beta-Amino Acids by Phenylalanine Aminomutase-Catalysed Amination of Cinnamic Acid Derivatives.
  Chembiochem, 10, 338-344.  
18454352 J.Song, and Z.Wang (2009).
Molecular cloning, expression and characterization of a phenylalanine ammonia-lyase gene (SmPAL1) from Salvia miltiorrhiza.
  Mol Biol Rep, 36, 939-952.  
19043702 K.V.Kiselev, A.S.Dubrovina, and V.P.Bulgakov (2009).
Phenylalanine ammonia-lyase and stilbene synthase gene expression in rolB transgenic cell cultures of Vitis amurensis.
  Appl Microbiol Biotechnol, 82, 647-655.  
19082600 S.McInnis, S.Clemens, and A.R.Kermode (2009).
The ornamental variety, Japanese striped corn, contains high anthocyanin levels and PAL specific activity: establishing the potential for development of an oral therapeutic.
  Plant Cell Rep, 28, 503-515.  
18556022 L.Wang, A.Gamez, H.Archer, E.E.Abola, C.N.Sarkissian, P.Fitzpatrick, D.Wendt, Y.Zhang, M.Vellard, J.Bliesath, S.M.Bell, J.F.Lemontt, C.R.Scriver, and R.C.Stevens (2008).
Structural and biochemical characterization of the therapeutic Anabaena variabilis phenylalanine ammonia lyase.
  J Mol Biol, 380, 623-635.  
18704907 N.Hoecker, T.Lamkemeyer, B.Sarholz, A.Paschold, C.Fladerer, J.Madlung, K.Wurster, M.Stahl, H.P.Piepho, A.Nordheim, and F.Hochholdinger (2008).
Analysis of nonadditive protein accumulation in young primary roots of a maize (Zea mays L.) F(1)-hybrid compared to its parental inbred lines.
  Proteomics, 8, 3882-3894.  
17240984 M.C.Moffitt, G.V.Louie, M.E.Bowman, J.Pence, J.P.Noel, and B.S.Moore (2007).
Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic and structural characterization.
  Biochemistry, 46, 1004-1012.
PDB codes: 2nyf 2nyn
17602252 Z.Xue, M.McCluskey, K.Cantera, F.S.Sariaslani, and L.Huang (2007).
Identification, characterization and functional expression of a tyrosine ammonia-lyase and its mutants from the photosynthetic bacterium Rhodobacter sphaeroides.
  J Ind Microbiol Biotechnol, 34, 599-604.  
16419141 C.Paizs, A.Katona, and J.Rétey (2006).
The interaction of heteroaryl-acrylates and alanines with phenylalanine ammonia-lyase from parsley.
  Chemistry, 12, 2739-2744.  
17185228 G.V.Louie, M.E.Bowman, M.C.Moffitt, T.J.Baiga, B.S.Moore, and J.P.Noel (2006).
Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases.
  Chem Biol, 13, 1327-1338.
PDB codes: 2o6y 2o78 2o7b 2o7d 2o7e 2o7f
17185227 K.T.Watts, B.N.Mijts, P.C.Lee, A.J.Manning, and C.Schmidt-Dannert (2006).
Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family.
  Chem Biol, 13, 1317-1326.  
16478474 S.Pilbák, A.Tomin, J.Rétey, and L.Poppe (2006).
The essential tyrosine-containing loop conformation and the role of the C-terminal multi-helix region in eukaryotic phenylalanine ammonia-lyases.
  FEBS J, 273, 1004-1019.  
15860421 J.P.Noel, M.B.Austin, and E.K.Bomati (2005).
Structure-function relationships in plant phenylpropanoid biosynthesis.
  Curr Opin Plant Biol, 8, 249-253.  
17193201 J.Zoń, P.Miziak, N.Amrhein, and R.Gancarz (2005).
Inhibitors of phenylalanine ammonia-lyase (PAL): synthesis and biological evaluation of 5-substituted 2-aminoindane-2-phosphonic acids.
  Chem Biodivers, 2, 1187-1194.  
15906398 L.Poppe, and J.Rétey (2005).
Friedel-Crafts-type mechanism for the enzymatic elimination of ammonia from histidine and phenylalanine.
  Angew Chem Int Ed Engl, 44, 3668-3688.  
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 code is shown on the right.