9CJX | pdb_00009cjx

Solution NMR structure of the RiPP proteusin DprE2 from Desulfotomaculum sp.

• PDB DOI: https://doi.org/10.2210/pdb9CJX/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Desulfotomaculum sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-08 Released: 2024-12-04 
• Deposition Author(s): McShan, A.C., Agarwal, V., Vidya, F.N.U.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Large protein-like leader peptides engage differently with RiPP halogenases and lanthionine synthetases.

Vidya, F., Luo, Y., Wu, H., van der Donk, W.A., McShan, A.C., Agarwal, V.

(2025) Nat Commun 16: 9273-9273

• PubMed: 41115907 
• DOI: https://doi.org/10.1038/s41467-025-64365-3
• Primary Citation of Related Structures:  
  9CJX


• PubMed Abstract: 
  

  The biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs) involves binding of the N-terminal leader region of precursor peptides to peptide-modifying enzymes and subsequent modification of the C-terminal core. Canonical RiPP leaders are short and unstructured. However, atypical RiPP leaders called nitrile hydratase-like leader peptides (NHLPs) are longer and structured. The sequence and structural divergence dictate that the NHLPs engage with peptide modifying enzymes using binding modes that are distinct from that for the canonical short leader peptides. Here, we investigate the molecular basis of NHLP engagement with class II lanthionine synthetases (LanMs). Using genome mining, we identify a LanM that is selective for the NHLP while modifying diverse core peptides. The solution NMR structure of the NHLP reveals a rigid tertiary fold. Biochemically verified computational models support a bimodal mechanism for NHLP binding to LanMs. Findings developed here illuminate unique protein-protein interaction modalities that guide RiPP biosynthesis.

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Organizational Affiliation: 
• School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA. [e-mail].
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA. [e-mail].
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 11.45 kDa 
• Atom Count: 641 
• Modeled Residue Count: 86 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NHLP leader peptide family natural product	A	107	Desulfotomaculum sp.	Mutation(s): 0  Gene Names: DEF36_00885

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): McShan, A.C., Agarwal, V., Vidya, F.N.U.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM142882

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release
  
• Version 1.1: 2024-12-11
  Changes: Data collection, Refinement description
• Version 1.2: 2025-12-17
  Changes: Database references