8D0S

Human FUT9 bound to GDP and LNnT

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2022-05-26 Released: 2023-05-24 
  • Deposition Author(s): Kadirvelraj, R., Wood, Z.A.
  • Funding Organization(s): National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for Lewis antigen synthesis by the alpha 1,3-fucosyltransferase FUT9.

Kadirvelraj, R.Boruah, B.M.Wang, S.Chapla, D.Huang, C.Ramiah, A.Hudson, K.L.Prudden, A.R.Boons, G.J.Withers, S.G.Wood, Z.A.Moremen, K.W.

(2023) Nat Chem Biol 19: 1022-1030

  • DOI: https://doi.org/10.1038/s41589-023-01345-y
  • Primary Citation of Related Structures:  
    8D0O, 8D0P, 8D0Q, 8D0R, 8D0S, 8D0U, 8D0W, 8D0X

  • PubMed Abstract: 

    Mammalian cell surface and secreted glycoproteins exhibit remarkable glycan structural diversity that contributes to numerous physiological and pathogenic interactions. Terminal glycan structures include Lewis antigens synthesized by a collection of α1,3/4-fucosyltransferases (CAZy GT10 family). At present, the only available crystallographic structure of a GT10 member is that of the Helicobacter pylori α1,3-fucosyltransferase, but mammalian GT10 fucosyltransferases are distinct in sequence and substrate specificity compared with the bacterial enzyme. Here, we determined crystal structures of human FUT9, an α1,3-fucosyltransferase that generates Lewis x and Lewis y antigens, in complex with GDP, acceptor glycans, and as a FUT9-donor analog-acceptor Michaelis complex. The structures reveal substrate specificity determinants and allow prediction of a catalytic model supported by kinetic analyses of numerous active site mutants. Comparisons with other GT10 fucosyltransferases and GT-B fold glycosyltransferases provide evidence for modular evolution of donor- and acceptor-binding sites and specificity for Lewis antigen synthesis among mammalian GT10 fucosyltransferases.


  • Organizational Affiliation

    Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9322Homo sapiensMutation(s): 1 
Gene Names: FUT9
EC: 2.4.1.152
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y231 (Homo sapiens)
Explore Q9Y231 
Go to UniProtKB:  Q9Y231
PHAROS:  Q9Y231
GTEx:  ENSG00000172461 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y231
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9Y231-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose
C
3N/A
Glycosylation Resources
GlyTouCan:  G06580KR
GlyCosmos:  G06580KR
GlyGen:  G06580KR
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
D [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
GDP BindingDB:  8D0S Ki: 7.79e+4 (nM) from 1 assay(s)
IC50: 5.90e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.16α = 90
b = 127.16β = 90
c = 127.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

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 on Alcohol Abuse and Alcoholism (NIH/NIAAA)United StatesGM130915, GM103390 and P01GM107012

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references
  • Version 1.2: 2023-08-09
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description