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 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UDPClick on this verticalbar to view detailsBest fitted GZLClick on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view details

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
Expand
  • 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]
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 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UDPClick on this verticalbar to view detailsBest fitted GZLClick on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view details

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