2W2A

Crystal Structure of 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: 1.38 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 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.De Las 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:  
    2WSJ, 2W2F, 2W2A, 2W2B

  • 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 remains largely unknown ...

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
P-COUMARIC ACID DECARBOXYLASEA, B194Lactiplantibacillus plantarumMutation(s): 0 
EC: 4.1.1
Find proteins for F9ULL2 (Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1))
Explore F9ULL2 
Go to UniProtKB:  F9ULL2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.181α = 90
b = 43.181β = 90
c = 232.498γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-11-09
    Changes: Database references, Derived calculations