Crocagin methyl transferase CgnL

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


Unusual peptide-binding proteins guide pyrroloindoline alkaloid formation in crocagin biosynthesis.

Adam, S.Zheng, D.Klein, A.Volz, C.Mullen, W.Shirran, S.L.Smith, B.O.Kalinina, O.V.Muller, R.Koehnke, J.

(2023) Nat Chem 15: 560-568

  • DOI: https://doi.org/10.1038/s41557-023-01153-w
  • Primary Citation of Related Structures:  
    6ZSU, 6ZSV, 7PD7, 8A2N

  • PubMed Abstract: 

    Ribosomally synthesized and post-translationally modified peptide natural products have provided many highly unusual scaffolds. This includes the intriguing alkaloids crocagins, which possess a tetracyclic core structure and whose biosynthesis has remained enigmatic. Here we use in vitro experiments to demonstrate that three proteins, CgnB, CgnC and CgnE, are sufficient for the production of the hallmark tetracyclic crocagin core from the precursor peptide CgnA. The crystal structures of the homologues CgnB and CgnE reveal them to be the founding members of a peptide-binding protein family and allow us to rationalize their distinct functions. We further show that the hydrolase CgnD liberates the crocagin core scaffold, which is subsequently N-methylated by CgnL. These insights allow us to propose a biosynthetic scheme for crocagins. Bioinformatic analyses based on these data led to the discovery of related biosynthetic pathways that may provide access to a structurally diverse family of peptide-derived pyrroloindoline alkaloids.

  • Organizational Affiliation

    Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Saarbrücken, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
255Chondromyces crocatusMutation(s): 0 
Gene Names: CMC5_025500
Find proteins for A0A0K1EC20 (Chondromyces crocatus)
Explore A0A0K1EC20 
Go to UniProtKB:  A0A0K1EC20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K1EC20
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth C],
O [auth D]
C14 H20 N6 O5 S
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth A]
I [auth B]
K [auth B]
E [auth A],
F [auth A],
H [auth A],
I [auth B],
K [auth B],
L [auth C],
M [auth C]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.947α = 90
b = 128.117β = 90.393
c = 94.295γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101002326

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2023-03-22
    Changes: Database references
  • Version 1.3: 2023-04-12
    Changes: Database references
  • Version 1.4: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-02-28
    Changes: Database references