The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3)

Experimental Data Snapshot

  • Resolution: 3.08 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

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This is version 1.3 of the entry. See complete history


Comparison of glycoside hydrolase family 3 beta-xylosidases from basidiomycetes and ascomycetes reveals evolutionarily distinct xylan degradation systems.

Kojima, K.Sunagawa, N.Mikkelsen, N.E.Hansson, H.Karkehabadi, S.Samejima, M.Sandgren, M.Igarashi, K.

(2022) J Biol Chem 298: 101670-101670

  • DOI: https://doi.org/10.1016/j.jbc.2022.101670
  • Primary Citation of Related Structures:  
    7VC6, 7VC7

  • PubMed Abstract: 

    Xylan is the most common hemicellulose in plant cell walls, though the structure of xylan polymers differs between plant species. Here, to gain a better understanding of fungal xylan degradation systems, which can enhance enzymatic saccharification of plant cell walls in industrial processes, we conducted a comparative study of two glycoside hydrolase family 3 (GH3) β-xylosidases (Bxls), one from the basidiomycete Phanerochaete chrysosporium (PcBxl3), and the other from the ascomycete Trichoderma reesei (TrXyl3A). A comparison of the crystal structures of the two enzymes, both with saccharide bound at the catalytic center, provided insight into the basis of substrate binding at each subsite. PcBxl3 has a substrate-binding pocket at subsite -1, while TrXyl3A has an extra loop that contains additional binding subsites. Furthermore, kinetic experiments revealed that PcBxl3 degraded xylooligosaccharides faster than TrXyl3A, while the K M values of TrXyl3A were lower than those of PcBxl3. The relationship between substrate specificity and degree of polymerization of substrates suggested that PcBxl3 preferentially degrades xylobiose (X 2 ), while TrXyl3A degrades longer xylooligosaccharides. Moreover, docking simulation supported the existence of extended positive subsites of TrXyl3A in the extra loop located at the N-terminus of the protein. Finally, phylogenetic analysis suggests that wood-decaying basidiomycetes use Bxls such as PcBxl3 that act efficiently on xylan structures from woody plants, whereas molds use instead Bxls that efficiently degrade xylan from grass. Our results provide added insights into fungal efficient xylan degradation systems.

  • Organizational Affiliation

    Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
xylan 1,4-beta-xylosidase743Phanerodontia chrysosporiumMutation(s): 0 
Gene Names: PcBxl3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1PE

Download Ideal Coordinates CCD File 
B [auth A]
G [auth A]
I [auth A]
J [auth A]
K [auth A]
B [auth A],
G [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],
Q [auth A],
R [auth A]
C10 H22 O6
Query on NAG

Download Ideal Coordinates CCD File 
T [auth A]
U [auth A]
V [auth A]
W [auth A]
X [auth A]
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
C8 H15 N O6
XYP (Subject of Investigation/LOI)
Query on XYP

Download Ideal Coordinates CCD File 
AA [auth A]beta-D-xylopyranose
C5 H10 O5
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth A],
H [auth A],
S [auth A]
C4 H10 O3
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.08 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.367α = 90
b = 91.071β = 90
c = 106.012γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19H03013
Japan Society for the Promotion of Science (JSPS)Japan19K15884
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan18H05494

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-04-13
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description