6J31

Crystal Structure Analysis of the Glycotransferase of kitacinnamycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Genome mining and biosynthesis of kitacinnamycins as a STING activator.

Shi, J.Liu, C.L.Zhang, B.Guo, W.J.Zhu, J.Chang, C.Y.Zhao, E.J.Jiao, R.H.Tan, R.X.Ge, H.M.

(2019) Chem Sci 10: 4839-4846

  • DOI: https://doi.org/10.1039/c9sc00815b
  • Primary Citation of Related Structures:  
    6J31, 6J32

  • PubMed Abstract: 

    Cinnamoyl-containing nonribosomal peptides (CCNPs) are a small group of secondary metabolites with potent biological activities produced by actinobacteria. Two remarkable features in the biosynthesis of CCNPs include the nonribosomal peptide synthases (NRPSs) for assembly of the depsipeptide backbone and the type II polyketide synthases (PKSs) for N-terminal cinnamoyl moiety construction. Here, we present a genome mining approach targeting both NRPS and type II PKS for discovery of new CCNPs, which led to the identification of 51 putative CCNP gene clusters from public bacterial genome databases. After strain prioritization, a novel class of CCNP-type glycopeptides named kitacinnamycins, one of which showing potent activation ability towards the stimulator of interferon genes (STING) protein, was identified. Bioinformatic, genetic and biochemical analysis revealed the use of the NRPS assembly line to form the macrocyclic peptide backbone, followed by a P450 monooxygenase to generate terminal oxidized groups. A glycosyltransferase with relatively broad substrate specificity transfers sugars to the newly generated OH/COOH group. The protein crystallographic study further provided structural insights into this glycosylation. Our results not only demonstrated the feasibility of genome mining and strain prioritization for the discovery of new bioactive natural products but also disclosed the biosynthetic pathway for kitacinnamycins.


  • Organizational Affiliation

    State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , School of Life Sciences , Nanjing University , 210023 , P. R. China . Email: rxtan@nju.edu.cn ; Email: hmge@nju.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
kcn28
A, B, C, D
396KitasatosporaMutation(s): 0 
UniProt
Find proteins for A0A514S208 (Kitasatospora sp)
Explore A0A514S208 
Go to UniProtKB:  A0A514S208
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A514S208
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE
E, F, G, H
9synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 243.16α = 90
b = 243.16β = 90
c = 243.16γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China81522042, 21572100, 81773591, 81530089, 81673333, 81803380, 21861142005, 21761142001, 21661140001

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2024-07-10
    Changes: Polymer sequence