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

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View more in-depth experimental data

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