7VC7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

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.


Macromolecules
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
EC: 3.2.1.37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
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]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
NAG
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]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
XYP (Subject of Investigation/LOI)
Query on XYP

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

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth A],
H [auth A],
S [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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
  • Version 1.4: 2024-11-20
    Changes: Structure summary