6VLD

Crystal structure of human alpha 1,6-fucosyltransferase, FUT8 bound to GDP and A2SGP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural basis of substrate recognition and catalysis by fucosyltransferase 8.

Jarva, M.A.Dramicanin, M.Lingford, J.P.Mao, R.John, A.Jarman, K.E.Grinter, R.Goddard-Borger, E.D.

(2020) J Biol Chem 295: 6677-6688

  • DOI: 10.1074/jbc.RA120.013291
  • Primary Citation of Related Structures:  
    6VLE, 6VLD, 6VLG, 6VLF

  • PubMed Abstract: 
  • Fucosylation of the innermost GlcNAc of N -glycans by fucosyltransferase 8 (FUT8) is an important step in the maturation of complex and hybrid N -glycans. This simple modification can dramatically affect the activities and half-lives of glycoproteins, effects that are relevant to understanding the invasiveness of some cancers, development of mAb therapeutics, and the etiology of a congenital glycosylation disorder ...

    Fucosylation of the innermost GlcNAc of N -glycans by fucosyltransferase 8 (FUT8) is an important step in the maturation of complex and hybrid N -glycans. This simple modification can dramatically affect the activities and half-lives of glycoproteins, effects that are relevant to understanding the invasiveness of some cancers, development of mAb therapeutics, and the etiology of a congenital glycosylation disorder. The acceptor substrate preferences of FUT8 are well-characterized and provide a framework for understanding N -glycan maturation in the Golgi; however, the structural basis of these substrate preferences and the mechanism through which catalysis is achieved remain unknown. Here we describe several structures of mouse and human FUT8 in the apo state and in complex with GDP, a mimic of the donor substrate, and with a glycopeptide acceptor substrate at 1.80-2.50 Å resolution. These structures provide insights into a unique conformational change associated with donor substrate binding, common strategies employed by fucosyltransferases to coordinate GDP, features that define acceptor substrate preferences, and a likely mechanism for enzyme catalysis. Together with molecular dynamics simulations, the structures also revealed how FUT8 dimerization plays an important role in defining the acceptor substrate-binding site. Collectively, this information significantly builds on our understanding of the core fucosylation process.


    Organizational Affiliation

    Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-(1,6)-fucosyltransferaseA, B, C [auth G], D [auth H]481Homo sapiensMutation(s): 0 
Gene Names: FUT8
EC: 2.4.1.68
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYC5 (Homo sapiens)
Explore Q9BYC5 
Go to UniProtKB:  Q9BYC5
PHAROS:  Q9BYC5
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-glucopyranoseE [auth C], F [auth D], G [auth E], H [auth F]7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G39213VZ
GlyCosmos:  G39213VZ
GlyGen:  G39213VZ
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
J [auth A], P [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ASN (Subject of Investigation/LOI)
Query on ASN

Download Ideal Coordinates CCD File 
I [auth A], O [auth B], R [auth G], U [auth H]ASPARAGINE
C4 H8 N2 O3
DCXYFEDJOCDNAF-REOHCLBHSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A] , L [auth A] , M [auth A] , N [auth A] , Q [auth B] , S [auth G] , T [auth G] , V [auth H] , 
K [auth A],  L [auth A],  M [auth A],  N [auth A],  Q [auth B],  S [auth G],  T [auth G],  V [auth H],  W [auth H],  X [auth H],  Y [auth H],  Z [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.307α = 90
b = 68.453β = 111.21
c = 249.983γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata 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
Other governmentAustraliaGNT1139546

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-09-16
    Changes: Database references, Derived calculations, Structure summary