8D0O | pdb_00008d0o

Human alpha1,3-fucosyltransferase FUT9, heavy atom derivative

  • 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: 2.10 Å
  • R-Value Free: 
    0.209 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8D0O

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 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.

Macromolecule Content 

  • Total Structure Weight: 41.25 kDa 
  • Atom Count: 2,769 
  • Modeled Residue Count: 297 
  • Deposited Residue Count: 322 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CS
(Subject of Investigation/LOI)

Query on CS



Download:Ideal Coordinates CCD File
Q [auth A]
R [auth A]
S [auth A]
T [auth A]
U [auth A]
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
IOD
(Subject of Investigation/LOI)

Query on IOD



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [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]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.209 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.12α = 90
b = 127.12β = 90
c = 127.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2023-06-07
    Changes: Database references
  • Version 1.2: 2023-08-09
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary