5LTM

Crystal structure of phenylalanine ammonia-lyase from Anabaena variabilis (Y78F-C503S-C565S) bound to cinnamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.413 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Zymophore identification enables the discovery of novel phenylalanine ammonia lyase enzymes.

Weise, N.J.Ahmed, S.T.Parmeggiani, F.Galman, J.L.Dunstan, M.S.Charnock, S.J.Leys, D.Turner, N.J.

(2017) Sci Rep 7: 13691-13691

  • DOI: 10.1038/s41598-017-13990-0

  • PubMed Abstract: 
  • The suite of biological catalysts found in Nature has the potential to contribute immensely to scientific advancements, ranging from industrial biotechnology to innovations in bioenergy and medical intervention. The endeavour to obtain a catalyst of ...

    The suite of biological catalysts found in Nature has the potential to contribute immensely to scientific advancements, ranging from industrial biotechnology to innovations in bioenergy and medical intervention. The endeavour to obtain a catalyst of choice is, however, wrought with challenges. Herein we report the design of a structure-based annotation system for the identification of functionally similar enzymes from diverse sequence backgrounds. Focusing on an enzymatic activity with demonstrated synthetic and therapeutic relevance, five new phenylalanine ammonia lyase (PAL) enzymes were discovered and characterised with respect to their potential applications. The variation and novelty of various desirable traits seen in these previously uncharacterised enzymes demonstrates the importance of effective sequence annotation in unlocking the potential diversity that Nature provides in the search for tailored biological tools. This new method has commercial relevance as a strategy for assaying the 'evolvability' of certain enzyme features, thus streamlining and informing protein engineering efforts.


    Organizational Affiliation

    School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phenylalanine ammonia lyase
B, A
539Anabaena variabilis (strain ATCC 29413 / PCC 7937)Mutation(s): 0 
EC: 4.3.1.24
Find proteins for Q3M5Z3 (Anabaena variabilis (strain ATCC 29413 / PCC 7937))
Go to UniProtKB:  Q3M5Z3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HCI
Query on HCI

Download SDF File 
Download CCD File 
A, B
HYDROCINNAMIC ACID
3PP; 3-PHENYLPROPIONIC ACID
C9 H10 O2
XMIIGOLPHOKFCH-UHFFFAOYSA-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: 2.413 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.156 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.077α = 90.00
b = 78.077β = 90.00
c = 354.492γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references
  • Version 1.2: 2018-10-24
    Type: Data collection, Source and taxonomy