7TWM | pdb_00007twm

Structure of a borosin methyltransferase from Mycena rosella with peptide CspL(MroMCspL) in complex with SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Bioconjugate Platform for Iterative Backbone N -Methylation of Peptides.

Zheng, Y.Ongpipattanakul, C.Nair, S.K.

(2022) ACS Catal 12: 14006-14014

  • DOI: https://doi.org/10.1021/acscatal.2c04681
  • Primary Citation Related Structures: 
    7TWK, 7TWL, 7TWM

  • PubMed Abstract: 

    N -methylation of peptide backbones has often been utilized as a strategy towards the development of peptidic drugs. However, difficulties in the chemical synthesis, high cost of enantiopure N -methyl building blocks, and subsequent coupling inefficiencies have hampered larger-scale medicinal chemical efforts. Here, we present a chemoenzymatic strategy for backbone N -methylation by bioconjugation of peptides of interest to the catalytic scaffold of a borosin-type methyltransferase. Crystal structures of a substrate tolerant enzyme from Mycena rosella guided the design of a decoupled catalytic scaffold that can be linked via a heterobifunctional crosslinker to any peptide substrate of choice. Peptides linked to the scaffold, including those with non-proteinogenic residues, show robust backbone N -methylation. Various crosslinking strategies were tested to facilitate substrate disassembly, which enabled a reversible bioconjugation approach that efficiently released modified peptide. Our results provide general framework for the backbone N -methylation on any peptide of interest and may facilitate the production of large libraries of N -methylated peptides.


  • Organizational Affiliation
    • Department of Biochemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana, IL, 61801, USA.

Macromolecule Content 

  • Total Structure Weight: 177.52 kDa 
  • Atom Count: 12,715 
  • Modeled Residue Count: 1,520 
  • Deposited Residue Count: 1,608 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MroMCspL
A, B, C, D
402Mycena rosellaMutation(s): 0 
UniProt
Find proteins for A0A9X9ZA30 (Mycena rosella)
Explore A0A9X9ZA30 
Go to UniProtKB:  A0A9X9ZA30
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9X9ZA30
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.96α = 90
b = 190.96β = 90
c = 93.589γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

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 StatesR01 GM079038

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Data collection, Structure summary