8YRL

Crystal structure of Aspergillus fumigatus Galactofuranosylransferase (AfGfsA) in complex with UDP and galactofuranose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Substrate binding and catalytic mechanism of UDP-alpha-D-galactofuranose: beta-galactofuranoside beta-(1→5)-galactofuranosyltransferase GfsA.

Oka, T.Okuno, A.Hira, D.Teramoto, T.Chihara, Y.Hirata, R.Kadooka, C.Kakuta, Y.

(2024) PNAS Nexus 3: pgae482-pgae482

  • DOI: https://doi.org/10.1093/pnasnexus/pgae482
  • Primary Citation of Related Structures:  
    8YRL

  • PubMed Abstract: 

    UDP-α-D-galactofuranose (UDP-Galf): β-galactofuranoside β-(1→5)-galactofuranosyltransferase, known as GfsA, is essential in synthesizing β-(1→5)-galactofuranosyl oligosaccharides that are incorporated into the cell wall of pathogenic fungi. This study analyzed the structure and function of GfsA from Aspergillus fumigatus . To provide crucial insights into the catalytic mechanism and substrate recognition, the complex structure was elucidated with manganese (Mn 2+ ), a donor substrate product (UDP), and an acceptor sugar molecule (β-galactofuranose). In addition to the typical GT-A fold domain, GfsA has a unique domain formed by the N and C termini. The former interacts with the GT-A of another GfsA, forming a dimer. The active center that contains Mn 2+ , UDP, and galactofuranose forms a groove structure that is highly conserved in the GfsA of Pezizomycotina fungi. Enzymatic assays using site-directed mutants were conducted to determine the roles of specific active-site residues in the enzymatic activity of GfsA. The predicted enzyme-substrate complex model containing UDP-Galf characterized a specific β-galactofuranosyltransfer mechanism to the 5'-OH of β-galactofuranose. Overall, the structure of GfsA in pathogenic fungi provides insights into the complex glycan biosynthetic processes of fungal pathogenesis and may inform the development of novel antifungal therapies.


  • Organizational Affiliation

    Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyltransferase family 31 protein
A, B
495Aspergillus fumigatus CEA10Mutation(s): 0 
Gene Names: AFUB_096220
UniProt
Find proteins for B0YDN6 (Aspergillus fumigatus (strain CBS 144.89 / FGSC A1163 / CEA10))
Explore B0YDN6 
Go to UniProtKB:  B0YDN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0YDN6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP (Subject of Investigation/LOI)
Query on UDP

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
GZL (Subject of Investigation/LOI)
Query on GZL

Download Ideal Coordinates CCD File 
K [auth A],
S [auth B]
beta-D-galactofuranose
C6 H12 O6
AVVWPBAENSWJCB-DGPNFKTASA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.142α = 90
b = 188.606β = 90
c = 71.933γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
XSCALEdata scaling
SOLVEphasing

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)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Database references