5KX6 | pdb_00005kx6

The structure of Arabidopsis thaliana FUT1 Mutant R284K in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.327 (Depositor), 0.327 (DCC) 
  • R-Value Work: 
    0.253 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 
    0.256 (Depositor) 

Starting Model: experimental
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This is version 1.4 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: 109.63 kDa 
  • Atom Count: 7,978 
  • Modeled Residue Count: 890 
  • Deposited Residue Count: 952 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galactoside 2-alpha-L-fucosyltransferase
A, B
476Arabidopsis thalianaMutation(s): 1 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.327 (Depositor), 0.327 (DCC) 
  • R-Value Work:  0.253 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 0.256 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.224α = 90
b = 112.957β = 104.48
c = 87.824γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing

Structure Validation

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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: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary