Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 247.05 kDa 
• Atom Count: 16261 
• Modelled Residue Count: 2048 
• Deposited Residue Count: 2260 
• Unique protein chains: 1

2NYN

Crystal structure of phenylalanine ammonia-lyase from Anabaena variabilis

• PDB DOI: 10.2210/pdb2NYN/pdb

• Classification: LYASE
• Organism(s): Trichormus variabilis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-11-21 Released: 2007-02-06 
• Deposition Author(s): Louie, G.V., Moffitt, M.C., Bowman, M.E., Pence, J., Noel, J.P., Moore, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.242 
• R-Value Work: 0.223 

Literature

Discovery of Two Cyanobacterial Phenylalanine Ammonia Lyases: Kinetic and Structural Characterization.

Moffitt, M.C., Louie, G.V., Bowman, M.E., Pence, J., Noel, J.P., Moore, B.S.

(2007) Biochemistry 46: 1004-1012

• PubMed: 17240984 
• DOI: 10.1021/bi061774g
• Primary Citation of Related Structures:  
  2NYF, 2NYN


• PubMed Abstract: 
  

Phenylalanine ammonia lyase (PAL) catalyzes the deamination of phenylalanine to cinnamate and ammonia. While PALs are common in terrestrial plants where they catalyze the first committed step in the formation of phenylpropanoids, only a few prokaryotic PALs have been identified to date. Here we describe for the first time PALs from cyanobacteria, in particular, Anabaena variabilis ATCC 29413 and Nostoc punctiforme ATCC 29133, identified by screening the genome sequences of these organisms for members of the aromatic amino acid ammonia lyase family. Both PAL genes associate with secondary metabolite biosynthetic gene clusters as observed for other eubacterial PAL genes. In comparison to eukaryotic homologues, the cyanobacterial PALs are 20% smaller in size but share similar substrate selectivity and kinetic activity toward L-phenylalanine over L-tyrosine. Structure elucidation by protein X-ray crystallography confirmed that the two cyanobacterial PALs are similar in tertiary and quatenary structure to plant and yeast PALs as well as the mechanistically related histidine ammonia lyases.

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Organizational Affiliation: 

Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanine/histidine ammonia-lyase	A, B, C, D	565	Trichormus variabilis	Mutation(s): 0  EC: 4.3.1.3 (PDB Primary Data), 4.3.1.24 (UniProt)
UniProt
Find proteins for Q3M5Z3 (Trichormus variabilis (strain ATCC 29413 / PCC 7937)) Explore Q3M5Z3  Go to UniProtKB:  Q3M5Z3

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MDO	A, B, C, D	L-PEPTIDE LINKING	C8 H11 N3 O3		ALA, SER, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.242 
• R-Value Work: 0.223 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.193	α = 103.52
b = 88.515	β = 97.82
c = 90.058	γ = 116.24

Software Package:

Software Name	Purpose
MOLREP	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-21 
• Released Date: 2007-02-06 
Deposition Author(s): Louie, G.V., Moffitt, M.C., Bowman, M.E., Pence, J., Noel, J.P., Moore, B.S.

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance