2VSU

A ternary complex of Hydroxycinnamoyl-CoA Hydratase-Lyase (HCHL) with acetyl-Coenzyme A and vanillin gives insights into substrate specificity and mechanism.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Ternary Complex of Hydroxycinnamoyl-Coa Hydratase-Lyase (Hchl) with Acetyl-Coa and Vanillin Gives Insights Into Substrate Specificity and Mechanism.

Bennett, J.P.Bertin, L.Moulton, B.Fairlamb, I.J.S.Brzozowski, A.M.Walton, N.J.Grogan, G.

(2008) Biochem.J. 414: 281

  • DOI: 10.1042/BJ20080714
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HCHL (hydroxycinnamoyl-CoA hydratase-lyase) catalyses the biotransformation of feruloyl-CoA to acetyl-CoA and the important flavour-fragrance compound vanillin (4-hydroxy-3-methoxybenzaldehyde) and is exploited in whole-cell systems for the bioconver ...

    HCHL (hydroxycinnamoyl-CoA hydratase-lyase) catalyses the biotransformation of feruloyl-CoA to acetyl-CoA and the important flavour-fragrance compound vanillin (4-hydroxy-3-methoxybenzaldehyde) and is exploited in whole-cell systems for the bioconversion of ferulic acid into natural equivalent vanillin. The reaction catalysed by HCHL has been thought to proceed by a two-step process involving first the hydration of the double bond of feruloyl-CoA and then the cleavage of the resultant beta-hydroxy thioester by retro-aldol reaction to yield the products. Kinetic analysis of active-site residues identified using the crystal structure of HCHL revealed that while Glu-143 was essential for activity, Ser-123 played no major role in catalysis. However, mutation of Tyr-239 to Phe greatly increased the K(M) for the substrate ferulic acid, fulfilling its anticipated role as a factor in substrate binding. Structures of WT (wild-type) HCHL and of the S123A mutant, each of which had been co-crystallized with feruloyl-CoA, reveal a subtle helix movement upon ligand binding, the consequence of which is to bring the phenolic hydroxyl of Tyr-239 into close proximity to Tyr-75 from a neighbouring subunit in order to bind the phenolic hydroxyl of the product vanillin, for which electron density was observed. The active-site residues of ligand-bound HCHL display a remarkable three-dimensional overlap with those of a structurally unrelated enzyme, vanillyl alcohol oxidase, that also recognizes p-hydroxylated aromatic substrates related to vanillin. The data both explain the observed substrate specificity of HCHL for p-hydroxylated cinnamate derivatives and illustrate a remarkable convergence of the molecular determinants of ligand recognition between the two otherwise unrelated enzymes.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
A, B, D
276Pseudomonas fluorescensMutation(s): 1 
EC: 4.1.2.41, 4.2.1.101
Find proteins for O69762 (Pseudomonas fluorescens)
Go to UniProtKB:  O69762
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
C
275Pseudomonas fluorescensMutation(s): 1 
EC: 4.1.2.41, 4.2.1.101
Find proteins for O69762 (Pseudomonas fluorescens)
Go to UniProtKB:  O69762
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
E
276Pseudomonas fluorescensMutation(s): 1 
EC: 4.1.2.41, 4.2.1.101
Find proteins for O69762 (Pseudomonas fluorescens)
Go to UniProtKB:  O69762
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
F
276Pseudomonas fluorescensMutation(s): 1 
EC: 4.1.2.41, 4.2.1.101
Find proteins for O69762 (Pseudomonas fluorescens)
Go to UniProtKB:  O69762
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download SDF File 
Download CCD File 
A, B, D, E, F
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
V55
Query on V55

Download SDF File 
Download CCD File 
D
4-hydroxy-3-methoxybenzaldehyde
C8 H8 O3
MWOOGOJBHIARFG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 90.081α = 90.00
b = 130.122β = 90.00
c = 144.743γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-08-03
    Type: Database references, Derived calculations, Non-polymer description