5B5S | pdb_00005b5s

Crystal structure of a carbohydrate esterase family 3 from Talaromyces cellulolyticus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.203 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

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This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of an acetylesterase from Talaromyces cellulolyticus and the importance of a disulfide bond near the active site

Watanabe, M., Fukada, H., Inoue, H., Ishikawa, K.

(2015) FEBS Lett 589: 1200-1206

  • DOI: https://doi.org/10.1016/j.febslet.2015.03.020
  • Primary Citation Related Structures: 
    5B5S

  • PubMed Abstract: 

    Carbohydrate esterase catalyzes the de-O or de-N-acylation of substituted saccharides in plant cell walls and thus has great potential for industrial biomass saccharification. We recently identified the putative carbohydrate esterase family 3 (CE3) from Talaromyces cellulolyticus. Here, we prepared the recombinant catalytic domain of the enzyme and crystallized it. The crystal structure was determined to 1.5 Å resolution. From the structural analysis, it was elucidated that a n-octyl-β-D-glucopyranoside bound to near the catalytic triad (Ser10, Asp179 and His182) and was buried in the active site cavity. Site-directed mutagenesis showed that the N-terminal disulfide bond located near the catalytic triad is involved in the activity and structural stability of the enzyme.

    • Organizational Affiliation: 
    • Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.

Macromolecule Content 

  • Total Structure Weight: 23.12 kDa 
  • Atom Count: 1,797 
  • Modeled Residue Count: 207 
  • Deposited Residue Count: 207 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetic acid207Talaromyces pinophilusMutation(s): 0 
Gene Names: axe, TCE0_004r00149
UniProt
Find proteins for A0A0A8IBJ8 (Talaromyces pinophilus)
Explore A0A0A8IBJ8 
Go to UniProtKB:  A0A0A8IBJ8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A8IBJ8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.203 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.905α = 90
b = 70.905β = 90
c = 87.093γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Structure summary