7LTE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis.

Miller, F.S.Crone, K.K.Jensen, M.R.Shaw, S.Harcombe, W.R.Elias, M.H.Freeman, M.F.

(2021) Nat Commun 12: 5355-5355

  • DOI: https://doi.org/10.1038/s41467-021-25575-7
  • Primary Citation of Related Structures:  
    7LTC, 7LTE, 7LTF, 7LTH, 7LTR, 7LTS

  • PubMed Abstract: 

    Peptide backbone α-N-methylations change the physicochemical properties of amide bonds to provide structural constraints and other favorable characteristics including biological membrane permeability to peptides. Borosin natural product pathways are the only known ribosomally encoded and posttranslationally modified peptides (RiPPs) pathways to incorporate backbone α-N-methylations on translated peptides. Here we report the discovery of type IV borosin natural product pathways (termed 'split borosins'), featuring an iteratively acting α-N-methyltransferase and separate precursor peptide substrate from the metal-respiring bacterium Shewanella oneidensis. A series of enzyme-precursor complexes reveal multiple conformational states for both α-N-methyltransferase and substrate. Along with mutational and kinetic analyses, our results give rare context into potential strategies for iterative maturation of RiPPs.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TP-methylase family protein
A, C
263Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: SO_1478
UniProt
Find proteins for Q8EGW3 (Shewanella oneidensis (strain 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
LigA domain-containing protein
B, D
71Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: SO_1479
UniProt
Find proteins for Q8EGW2 (Shewanella oneidensis (strain 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
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
IML
Query on IML
B, D
L-PEPTIDE LINKINGC7 H15 N O2ILE
MLE
Query on MLE
B, D
L-PEPTIDE LINKINGC7 H15 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.46α = 90
b = 108.66β = 94.1
c = 59.09γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2021-09-29
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description