2W2B

Crystal Structure of single point mutant Tyr20Phe p-coumaric Acid Decarboxylase from Lactobacillus plantarum: structural insights into the active site and decarboxylation catalytic mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

P-Coumaric Acid Decarboxylase from Lactobacillus Plantarum: Structural Insights Into the Active Site and Decarboxylation Catalytic Mechanism.

Rodriguez, H.Angulo, I.D Elas Rivas, B.Campillo, N.Paez, J.A.Munoz, R.Mancheno, J.M.

(2010) Proteins 78: 1662

  • DOI: 10.1002/prot.22684
  • Primary Citation of Related Structures:  
  • Also Cited By: 3NAD

  • PubMed Abstract: 
  • p-Coumaric acid decarboxylases (PDCs) catalyze the nonoxidative decarboxylation of hydroxycinnamic acids to generate the corresponding vinyl derivatives. Despite the biotechnological relevance of PDCs in food industry, their catalytic mechanism remai ...

    p-Coumaric acid decarboxylases (PDCs) catalyze the nonoxidative decarboxylation of hydroxycinnamic acids to generate the corresponding vinyl derivatives. Despite the biotechnological relevance of PDCs in food industry, their catalytic mechanism remains largely unknown. Here, we report insights into the structural basis of catalysis for the homodimeric PDC from Lactobacillus plantarum (LpPDC). The global fold of LpPDC is based on a flattened beta-barrel surrounding an internal cavity. Crystallographic and functional analyses of single-point mutants of residues located within this cavity have permitted identifying a potential substrate-binding pocket and also to provide structural evidences for rearrangements of surface loops so that they can modulate the accessibility to the active site. Finally, combination of the structural and functional data with in silico results enables us to propose a two-step catalytic mechanism for decarboxylation of p-coumaric acid by PDCs where Glu71 is involved in proton transfer, and Tyr18 and Tyr20 are involved in the proper substrate orientation and in the release of the CO(2) product.


    Organizational Affiliation

    Departamento de MicrobiologĂ­a, Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P-COUMARIC ACID DECARBOXYLASE
A, B
194Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)Mutation(s): 1 
Gene Names: padA
EC: 4.1.1.-
Find proteins for F9ULL2 (Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1))
Go to UniProtKB:  F9ULL2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, B
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.199 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 43.384α = 90.00
b = 43.384β = 90.00
c = 232.858γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-11-09
    Type: Database references, Derived calculations, Version format compliance