8XSG | pdb_00008xsg

Crystal structure of the Actinobacillus minor NM305 glucosyltransferase in complex with UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.201 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.159 (DCC) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

An uncharacterized gene from the Actinobacillus genus encodes a glucosyltransferase with successive transfer activity and unique substrate specificity.

Yamasaki, T.Kohda, D.

(2025) J Biological Chem 301: 108567-108567

  • DOI: https://doi.org/10.1016/j.jbc.2025.108567
  • Primary Citation of Related Structures:  
    8XSG, 8XSH

  • PubMed Abstract: 

    Elucidating the functions of glycosyltransferases is a necessary step toward understanding their biological roles and producing drug leads, cosmetics, and foods that utilize glycans as functional molecules. We found a previously uncharacterized protein classified as a glycosyltransferase encoded in the Actinobacillus minor NM305 genome and named the gene product A. minor glucoside-glucosyltransferase (AmGGT). To clarify the biochemical properties of the AmGGT protein, we determined its substrate specificity and crystal structure. AmGGT exhibited processive glycosyltransferase activity when UDP-Glc was used as the donor substrate and, unexpectedly, showed different acceptor substrate specificity from that of the homologous Agt proteins of other Actinobacillus species. While the homologous proteins transfer glucose residues to the nonreducing end of oligosaccharide chains linked to peptides, AmGGT cannot use glycopeptides as acceptors and requires the nonreducing end of oligosaccharides. The crystal structure provided clues to identify a sequence motif consisting of two pairs of two amino acid residues that defines the acceptor specificity, oligosaccharide, or glycopeptide. Based on this discovery, the acceptor substrate of AmGGT was changed from an oligosaccharide to a glycopeptide by transplanting the sequence motif from the homologous proteins. Furthermore, the AmGGT protein could utilize eukaryotic high-mannose type N-glycans as acceptors, as a model for branched oligosaccharides. The sequential glycosyltransfer activity and controllable substrate specificity of AmGGT will make it a useful tool in glycosyltransferase engineering to synthesize functional glycans and glycoconjugates.


  • Organizational Affiliation
    • Glyco-Biochemistry Laboratory, Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan. Electronic address: yamasaki.takahiro.u2@f.gifu-u.ac.jp.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative glycosyltransferase342Actinobacillus minor NM305Mutation(s): 0 
Gene Names: AM305_00150
UniProt
Find proteins for C5RYK2 (Actinobacillus minor NM305)
Explore C5RYK2 
Go to UniProtKB:  C5RYK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5RYK2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.201 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.136α = 90
b = 43.39β = 117.44
c = 95.823γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan23K14138

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Database references