1W27

Phenylalanine ammonia-lyase (PAL) from Petroselinum crispum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Entrance Into the Phenylpropanoid Metabolism Catalyzed by Phenylalanine Ammonia-Lyase

Ritter, H.Schulz, G.E.

(2004) Plant Cell 16: 3426

  • DOI: 10.1105/tpc.104.025288

  • PubMed 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 cr ...

    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.


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany 79104.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHENYLALANINE AMMONIA-LYASE 1
A, B
716Petroselinum crispumMutation(s): 0 
Gene Names: PAL1
EC: 4.3.1.24
Find proteins for P24481 (Petroselinum crispum)
Go to UniProtKB:  P24481
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTT
Query on DTT

Download SDF File 
Download CCD File 
A, B
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MDO
Query on MDO
A, B
L-PEPTIDE LINKINGC8 H11 N3 O3ALA, SER, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 119.960α = 90.00
b = 160.810β = 90.00
c = 141.330γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
RESOLVEphasing
XDSdata reduction
SHELXDphasing
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance