5CXX

Structure of a CE1 ferulic acid esterase, AmCE1/Fae1A, from Anaeromyces mucronatus in complex with Ferulic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Contributions of a unique beta-clamp to substrate recognition illuminates the molecular basis of exolysis in ferulic acid esterases.

Gruninger, R.J.Cote, C.McAllister, T.A.Abbott, D.W.

(2016) Biochem.J. 473: 839-849

  • DOI: 10.1042/BJ20151153
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lignocellulosic biomass is a promising renewable resource; however, deconstruction of this material is still the rate-limiting step. Major obstacles in the biocatalytic turnover of lignocellulose are ester-linked decorations that prevent access to pr ...

    Lignocellulosic biomass is a promising renewable resource; however, deconstruction of this material is still the rate-limiting step. Major obstacles in the biocatalytic turnover of lignocellulose are ester-linked decorations that prevent access to primary structural polysaccharides. Enzymes targeting these esters represent promising biotools for increasing bioconversion efficiency. Ruminant livestock are unique in their ability to degrade lignocellulose through the action of their gut microbiome. The anaerobic fungi (phylum Neocallimastigomycota) are key members of this ecosystem that express a large repertoire of carbohydrate-active enzymes (CAZymes) with little sequence identity with characterized CAZymes [Lombard, Golaconda, Drula, Coutinho and Henrissat (2014) Nucleic Acids Res. 42: , D490-D495]. We have identified a carbohydrate esterase family 1 (CE1) ferulic acid esterase (FAE) belonging to Anaeromyces mucronatus(AmCE1/Fae1a), and determined its X-ray structure in both the presence [1.55 Å (1 Å=0.1 nm)] and absence (1.60 Å) of ferulic acid. AmCE1 adopts an α/β-hydrolase fold that is structurally conserved with bacterial FAEs, and possesses a unique loop, termed the β-clamp, that encloses the ligand. Isothermal titration calorimetry reveals that substrate binding is driven by enthalpic contributions, which overcomes a large entropic penalty. A comparative analysis of AmCE1 with related enzymes has uncovered the apparent structural basis for differential FAE activities targeting cross-linking ferulic acid conjugates compared with terminal decorations. Based on comparisons to structurally characterized FAEs, we propose that the β-clamp may define the structural basis of exolytic activities in FAEs. This provides a structure-based tool for predicting exolysis and endolysis in CE1. These insights hold promise for rationally identifying enzymes tailored for bioconversion of biomass with variations in cell wall composition.


    Organizational Affiliation

    Lethbridge Research Centre, Agriculture and Agri-Food Canada, 5403-1st Ave South, Lethbridge, AB, Canada, T1J 4B1 robert.gruninger@agr.gc.ca wade.abbott@agr.gc.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ferulic acid esterase, AmCE1/Fae1A
A, B, C
275Anaeromyces mucronatusMutation(s): 0 
Gene Names: fae1A
EC: 3.1.1.73
Find proteins for F2YCB6 (Anaeromyces mucronatus)
Go to UniProtKB:  F2YCB6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A, B, C
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
FERULIC ACID
C10 H10 O4
KSEBMYQBYZTDHS-HWKANZROSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.141 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 99.790α = 90.00
b = 152.650β = 90.00
c = 154.120γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Author supporting evidence, Database references, Derived calculations