7Y4I

Crystal structure of SPINDLY in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural insights into mechanism and specificity of the plant protein O-fucosyltransferase SPINDLY.

Zhu, L.Wei, X.Cong, J.Zou, J.Wan, L.Xu, S.

(2022) Nat Commun 13: 7424-7424

  • DOI: https://doi.org/10.1038/s41467-022-35234-0
  • Primary Citation of Related Structures:  
    7Y4I

  • PubMed Abstract: 

    Arabidopsis glycosyltransferase family 41 (GT41) protein SPINDLY (SPY) plays pleiotropic roles in plant development. Despite the amino acid sequence is similar to human O-GlcNAc transferase, Arabidopsis SPY has been identified as a novel nucleocytoplasmic protein O-fucosyltransferase. SPY-like proteins extensively exist in diverse organisms, indicating that O-fucosylation by SPY is a common way to regulate intracellular protein functions. However, the details of how SPY recognizes and glycosylates substrates are unknown. Here, we present a crystal structure of Arabidopsis SPY/GDP complex at 2.85 Å resolution. SPY adopts a head-to-tail dimer. Strikingly, the conformation of a 'catalytic SPY'/GDP/'substrate SPY' complex formed by two symmetry-related SPY dimers is captured in the crystal lattice. The structure together with mutagenesis and enzymatic data demonstrate SPY can fucosylate itself and SPY's self-fucosylation region negatively regulates its enzyme activity, reveal SPY's substrate recognition and enzyme mechanism, and provide insights into the glycan donor substrate selection in GT41 proteins.


  • Organizational Affiliation

    Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
A, B
914Arabidopsis thalianaMutation(s): 1 
Gene Names: SPYAt3g11540F24K9.29
EC: 2.4.1.255 (PDB Primary Data), 2.4.1.221 (PDB Primary Data)
UniProt
Find proteins for Q96301 (Arabidopsis thaliana)
Explore Q96301 
Go to UniProtKB:  Q96301
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96301
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.735α = 90
b = 130.677β = 90
c = 141.368γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32000900

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description