RCSB PDB - 9CH0: Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-I65W) heteromeric complex (bound to SAH)

 9CH0

Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-I65W) heteromeric complex (bound to SAH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.327 (Depositor), 0.352 (DCC) 
  • R-Value Work:  0.292 (Depositor), 0.323 (DCC) 
  • R-Value Observed: 0.294 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

alpha-N-Methyltransferase regiospecificity is mediated by proximal, redundant enzyme-substrate interactions.

Crone, K.K.Labonte, J.W.Elias, M.H.Freeman, M.F.

(2025) Protein Sci 34: e70021-e70021

  • DOI: https://doi.org/10.1002/pro.70021
  • Primary Citation of Related Structures:  
    9CGW, 9CH0, 9CH1, 9CH2, 9CH3, 9CH5, 9CH7, 9CHI, 9CHK

  • PubMed Abstract: 

    N-Methylation of the peptide backbone confers pharmacologically beneficial characteristics to peptides that include greater membrane permeability and resistance to proteolytic degradation. The borosin family of ribosomally synthesized and post-translationally modified peptides offer a post-translational route to install amide backbone α-N-methylations. Previous work has elucidated the substrate scope and engineering potential of two examples of type I borosins, which feature autocatalytic precursors that encode N-methyltransferases that methylate their own C-termini in trans. We recently reported the first discrete N-methyltransferase and precursor peptide from Shewanella oneidensis MR-1, a minimally iterative, type IV borosin that allowed the first detailed kinetic analyses of borosin N-methyltransferases. Herein, we characterize the substrate scope and resilient regiospecificity of this discrete N-methyltransferase by comparison of relative rates and methylation patterns of over 40 precursor peptide variants along with structure analyses of nine enzyme-substrate complexes. Sequences critical to methylation are identified and demonstrated in assaying minimal peptide substrates and non-native peptide sequences for assessment of secondary structure requirements and engineering potential. This work grants understanding towards the mechanism of substrate recognition and iterative activity by discrete borosin N-methyltransferases.


  • Organizational Affiliation

    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, St. Paul, Minnesota, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TP-methylase family proteinA,
C,
E [auth H],
G [auth J]
263Shewanella oneidensisMutation(s): 0 
Gene Names: SO_1478
UniProt
Find proteins for Q8EGW3 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EGW3 
Go to UniProtKB:  Q8EGW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EGW3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
B, D
78Shewanella oneidensisMutation(s): 1 
Gene Names: SO_1479
UniProt
Find proteins for Q8EGW2 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EGW2 
Go to UniProtKB:  Q8EGW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EGW2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing proteinF [auth I],
H [auth K]
78Shewanella oneidensisMutation(s): 1 
Gene Names: SO_1479
UniProt
Find proteins for Q8EGW2 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EGW2 
Go to UniProtKB:  Q8EGW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EGW2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.327 (Depositor), 0.352 (DCC) 
  • R-Value Work:  0.292 (Depositor), 0.323 (DCC) 
  • R-Value Observed: 0.294 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.13α = 90.01
b = 108.02β = 93.41
c = 58.59γ = 89.95
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAHClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133475

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Derived calculations