1WB4

S954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with sinapinate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.111 
  • R-Value Observed: 0.113 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Molecular Determinants of Substrate Specificity in the Feruloyl Esterase Module of Xylanase 10B from Clostridium Thermocellum

Tarbouriech, N.Prates, J.A.Fontes, C.Davies, G.J.

(2005) Acta Crystallogr D Biol Crystallogr 61: 194

  • DOI: https://doi.org/10.1107/S0907444904029695
  • Primary Citation of Related Structures:  
    1WB4, 1WB5, 1WB6

  • PubMed Abstract: 

    Feruloyl esterases play a key role in the degradation of the intricate structure of the plant cell wall by hydrolysing the ferulate ester groups involved in the cross-linking between hemicelluloses and between hemicellulose and lignin. The structure of the feruloyl esterase module of Clostridium thermocellum cellulosomal xylanase 10B has been reported previously. It displays the alpha/beta hydrolase fold with a classical Ser-His-Asp catalytic triad. Here, the structures of a Ser-Ala mutant of this feruloyl esterase in complexes with methyl syringate, methyl sinapinate and methyl vanillate are described. Substrate binding is accompanied by subtle conformational changes at amino acids Trp982, Met955, Asn1023 and Ile1019 in the ligand-binding cavity. The structural determinants, particularly the m-methoxy substituent, governing the substrate specificity of Xyn10B feruloyl esterase are rationalized.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENDO-1,4-BETA-XYLANASE Y
A, B
297Acetivibrio thermocellusMutation(s): 1 
EC: 3.2.1.8
UniProt
Find proteins for P51584 (Acetivibrio thermocellus)
Explore P51584 
Go to UniProtKB:  P51584
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51584
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SXX
Query on SXX

Download Ideal Coordinates CCD File 
C [auth A],
Q [auth B]
SINAPINATE
C11 H12 O5
PCMORTLOPMLEFB-ONEGZZNKSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
G [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
R [auth B]
S [auth B]
T [auth B]
D [auth A],
E [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
F [auth A],
V [auth B]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.111 
  • R-Value Observed: 0.113 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.066α = 90
b = 108.405β = 90
c = 113.18γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description