LahSb - C-terminal methyltransferase involved in RiPP biosynthesis

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

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This is version 1.3 of the entry. See complete history


Characterization of a Dehydratase and Methyltransferase in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides in Lachnospiraceae.

Huo, L.Zhao, X.Acedo, J.Z.Estrada, P.Nair, S.K.van der Donk, W.A.

(2020) Chembiochem 21: 190-199

  • DOI: https://doi.org/10.1002/cbic.201900483
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    As a result of the exponential increase in genomic data, discovery of novel ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) has progressed rapidly in the past decade. The lanthipeptides are a major subset of RiPPs. Through genome mining we identified a novel lanthipeptide biosynthetic gene cluster (lah) from Lachnospiraceae bacterium C6A11, an anaerobic bacterium that is a member of the human microbiota and which is implicated in the development of host disease states such as type 2 diabetes and resistance to Clostridium difficile colonization. The lah cluster encodes at least seven putative precursor peptides and multiple post-translational modification (PTM) enzymes. Two unusual class II lanthipeptide synthetases LahM1/M2 and a substrate-tolerant S-adenosyl-l-methionine (SAM)-dependent methyltransferase LahS B are biochemically characterized in this study. We also present the crystal structure of LahS B in complex with product S-adenosylhomocysteine. This study sets the stage for further exploration of the final products of the lah pathway as well as their potential physiological functions in human/animal gut microbiota.

  • Organizational Affiliation

    Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SAM dependent methyltransferase LahSB308Lachnospiraceae bacterium C6A11Mutation(s): 0 
Gene Names: DEO87_04690
Find proteins for A0A3D0LE54 (Lachnospiraceae bacterium)
Explore A0A3D0LE54 
Go to UniProtKB:  A0A3D0LE54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3D0LE54
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SAH

Download Ideal Coordinates CCD File 
C14 H20 N6 O5 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.729α = 90
b = 115.729β = 90
c = 71.26γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
pointlessdata scaling

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2020-02-05
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references