6DRU

Xylosidase from Aspergillus niger


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history


Literature

Crystal Structure of alpha-Xylosidase fromAspergillus nigerin Complex with a Hydrolyzed Xyloglucan Product and New Insights in Accurately Predicting Substrate Specificities of GH31 Family Glycosidases.

Cao, H.Walton, J.D.Brumm, P.Phillips Jr., G.N.

(2020) ACS Sustain Chem Eng 8: 2540-2547

  • DOI: https://doi.org/10.1021/acssuschemeng.9b07073
  • Primary Citation of Related Structures:  
    6DRU

  • PubMed Abstract: 

    Glycoside hydrolase family 31 (GH31) enzymes show both highly conserved folds and catalytic residues. Yet different members of GH31 show very different substrate specificities, and it is not obvious how these specificities arise from the protein sequences. The fungal α-xylosidase, AxlA, was originally isolated from a commercial enzyme mixture secreted by Aspergillus niger and was reported to have potential as a catalytic component in biomass deconstruction in the biofuel industry. We report here the crystal structure of AxlA in complex with its catalytic product, a hydrolyzed xyloglucan oligosaccharide. On the basis of our new structure, we provide the structural basis for AxlA's role in xyloglucan utilization and, more importantly, a new procedure to predict and differentiate C5 vs C6 sugar specific activities based on protein sequences of the functionally diverse GH31 family enzymes.


  • Organizational Affiliation

    BioSciences at Rice and Department of Chemistry, Rice University, Houston, Texas 77251, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyl hydrolases family 31 family protein
A, B
718Aspergillus nigerMutation(s): 0 
Gene Names: ATCC64974_10330CAN33_17365
EC: 3.2.1.177
UniProt
Find proteins for A2QTU5 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513))
Explore A2QTU5 
Go to UniProtKB:  A2QTU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2QTU5
Glycosylation
Glycosylation Sites: 7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68668TB
GlyCosmos:  G68668TB
GlyGen:  G68668TB
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, I
10N-Glycosylation
Glycosylation Resources
GlyTouCan:  G40702WU
GlyCosmos:  G40702WU
GlyGen:  G40702WU
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-[beta-D-glucopyranose-(1-4)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
F, J
5N/A
Glycosylation Resources
GlyTouCan:  G48327XE
GlyCosmos:  G48327XE
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
G
4N/A
Glycosylation Resources
GlyTouCan:  G40879YH
GlyCosmos:  G40879YH
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ
GlyCosmos:  G80966KZ
GlyGen:  G80966KZ
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
O [auth A]
Q [auth B]
K [auth A],
L [auth A],
M [auth A],
O [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
V [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
XYS
Query on XYS

Download Ideal Coordinates CCD File 
N [auth A],
U [auth B]
alpha-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
P [auth A],
W [auth B],
X [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.132α = 90
b = 146.132β = 90
c = 220.081γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54 GM079401
Department of Energy (DOE, United States)United StatesDE-FC02-07ER64494

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2020-03-25
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-10-21
    Changes: Data collection, Structure summary
  • Version 2.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 2.3: 2024-11-13
    Changes: Structure summary