5KWK | pdb_00005kwk

The structure of Arabidopsis thaliana FUT1 in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.289 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural, mutagenic and in silico studies of xyloglucan fucosylation in Arabidopsis thaliana suggest a water-mediated mechanism.

Urbanowicz, B.R.Bharadwaj, V.S.Alahuhta, M.Pena, M.J.Lunin, V.V.Bomble, Y.J.Wang, S.Yang, J.Y.Tuomivaara, S.T.Himmel, M.E.Moremen, K.W.York, W.S.Crowley, M.F.

(2017) Plant J 91: 931-949

  • DOI: https://doi.org/10.1111/tpj.13628
  • Primary Citation Related Structures: 
    5KOE, 5KWK, 5KX6

  • PubMed Abstract: 

    The mechanistic underpinnings of the complex process of plant polysaccharide biosynthesis are poorly understood, largely because of the resistance of glycosyltransferase (GT) enzymes to structural characterization. In Arabidopsis thaliana, a glycosyl transferase family 37 (GT37) fucosyltransferase 1 (AtFUT1) catalyzes the regiospecific transfer of terminal 1,2-fucosyl residues to xyloglucan side chains - a key step in the biosynthesis of fucosylated sidechains of galactoxyloglucan. We unravel the mechanistic basis for fucosylation by AtFUT1 with a multipronged approach involving protein expression, X-ray crystallography, mutagenesis experiments and molecular simulations. Mammalian cell culture expressions enable the sufficient production of the enzyme for X-ray crystallography, which reveals the structural architecture of AtFUT1 in complex with bound donor and acceptor substrate analogs. The lack of an appropriately positioned active site residue as a catalytic base leads us to propose an atypical water-mediated fucosylation mechanism facilitated by an H-bonded network, which is corroborated by mutagenesis experiments as well as detailed atomistic simulations.


  • Organizational Affiliation
    • Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.

Macromolecule Content 

  • Total Structure Weight: 110.81 kDa 
  • Atom Count: 8,696 
  • Modeled Residue Count: 897 
  • Deposited Residue Count: 952 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galactoside 2-alpha-L-fucosyltransferase
A, B
476Arabidopsis thalianaMutation(s): 0 
Gene Names: FUT1FT1MUR2At2g03220T18E12.11
EC: 2.4.1.69 (PDB Primary Data), 2.4.1 (UniProt)
UniProt
Find proteins for Q9SWH5 (Arabidopsis thaliana)
Explore Q9SWH5 
Go to UniProtKB:  Q9SWH5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SWH5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP



Download:Ideal Coordinates CCD File
C [auth A],
N [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
D [auth A],
O [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
M [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



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],
K [auth A],
L [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.289 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.933α = 90
b = 113.103β = 105.01
c = 87.781γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references, Structure summary
  • Version 1.2: 2018-05-30
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary