5KJU

Crystal structure of Arabidopsis thaliana HCT in complex with p-coumaroylshikimate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Dynamic Conformational States Dictate Selectivity toward the Native Substrate in a Substrate-Permissive Acyltransferase.

Levsh, O.Chiang, Y.C.Tung, C.F.Noel, J.P.Wang, Y.Weng, J.K.

(2016) Biochemistry 55: 6314-6326

  • DOI: 10.1021/acs.biochem.6b00887
  • Primary Citation of Related Structures:  5KJS, 5KJT, 5KJV, 5KJW

  • PubMed Abstract: 
  • Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (HCT) is an essential acyltransferase that mediates flux through plant phenylpropanoid metabolism by catalyzing a reaction between p-coumaroyl-CoA and shikimate, yet it also exhibits broad su ...

    Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (HCT) is an essential acyltransferase that mediates flux through plant phenylpropanoid metabolism by catalyzing a reaction between p-coumaroyl-CoA and shikimate, yet it also exhibits broad substrate permissiveness in vitro. How do enzymes like HCT avoid functional derailment by cellular metabolites that qualify as non-native substrates? Here, we combine X-ray crystallography and molecular dynamics to reveal distinct dynamic modes of HCT under native and non-native catalysis. We find that essential electrostatic and hydrogen-bonding interactions between the ligand and active site residues, permitted by active site plasticity, are elicited more effectively by shikimate than by other non-native substrates. This work provides a structural basis for how dynamic conformational states of HCT favor native over non-native catalysis by reducing the number of futile encounters between the enzyme and shikimate.


    Organizational Affiliation

    Whitehead Institute for Biomedical Research , 9 Cambridge Center, Cambridge, Massachusetts 02142, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Shikimate O-hydroxycinnamoyltransferase
A
433Arabidopsis thalianaGene Names: HST (HCT)
EC: 2.3.1.133
Find proteins for Q9FI78 (Arabidopsis thaliana)
Go to UniProtKB:  Q9FI78
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6TO
Query on 6TO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.171 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.480α = 90.00
b = 99.480β = 90.00
c = 82.560γ = 120.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Howard Hughes Medical InstituteUnited States--
Pew Scholar Program in the Biomedical SciencesUnited States--
Searle Scholars ProgramUnited States--

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references
  • Version 1.2: 2016-12-21
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence