5FAL

Crystal structure of PvHCT in complex with CoA and p-coumaroyl-shikimate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.861 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin.

Eudes, A.Pereira, J.H.Yogiswara, S.Wang, G.Teixeira Benites, V.Baidoo, E.E.Lee, T.S.Adams, P.D.Keasling, J.D.Loque, D.

(2016) Plant Cell.Physiol. 57: 568-579

  • DOI: 10.1093/pcp/pcw016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lignin poses a major challenge in the processing of plant biomass for agro-industrial applications. For bioengineering purposes, there is a pressing interest in identifying and characterizing the enzymes responsible for the biosynthesis of lignin. Hy ...

    Lignin poses a major challenge in the processing of plant biomass for agro-industrial applications. For bioengineering purposes, there is a pressing interest in identifying and characterizing the enzymes responsible for the biosynthesis of lignin. Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase (HCT; EC 2.3.1.133) is a key metabolic entry point for the synthesis of the most important lignin monomers: coniferyl and sinapyl alcohols. In this study, we investigated the substrate promiscuity of HCT from a bryophyte (Physcomitrella) and from five representatives of vascular plants (Arabidopsis, poplar, switchgrass, pine and Selaginella) using a yeast expression system. We demonstrate for these HCTs a conserved capacity to acylate with p-coumaroyl-CoA several phenolic compounds in addition to the canonical acceptor shikimate normally used during lignin biosynthesis. Using either recombinant HCT from switchgrass (PvHCT2a) or an Arabidopsis stem protein extract, we show evidence of the inhibitory effect of these phenolics on the synthesis of p-coumaroyl shikimate in vitro, which presumably occurs via a mechanism of competitive inhibition. A structural study of PvHCT2a confirmed the binding of a non-canonical acceptor in a similar manner to shikimate in the active site of the enzyme. Finally, we exploited in Arabidopsis the substrate flexibility of HCT to reduce lignin content and improve biomass saccharification by engineering transgenic lines that overproduce one of the HCT non-canonical acceptors. Our results demonstrate conservation of HCT substrate promiscuity and provide support for a new strategy for lignin reduction in the effort to improve the quality of plant biomass for forage and cellulosic biofuels.


    Organizational Affiliation

    Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase 2
A
448Panicum virgatumMutation(s): 0 
Find proteins for R9RYW2 (Panicum virgatum)
Go to UniProtKB:  R9RYW2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
SKT
Query on SKT

Download SDF File 
Download CCD File 
A
(3~{R},4~{R},5~{R})-5-[(~{E})-3-(4-hydroxyphenyl)prop-2-enoyl]oxy-3,4-bis(oxidanyl)cyclohexene-1-carboxylic acid
C16 H16 O7
GVECSFFLZYNEBO-PDXJTRCTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.861 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.771α = 90.00
b = 63.521β = 90.00
c = 154.481γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references