9QVS | pdb_00009qvs

Crystal structure of the CtaG_D144N variant from Ruminiclostridium cellulolyticum (P2(1)-small)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.182 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Distal peptide elongation by a protease-like ligase and two distinct carrier proteins.

Gude, F.Bohne, A.Dell, M.Franke, J.Dunbar, K.L.Groll, M.Hertweck, C.

(2026) Chem 12: None-None

  • DOI: https://doi.org/10.1016/j.chempr.2025.102740
  • Primary Citation of Related Structures:  
    9QUZ, 9QVJ, 9QVK, 9QVL, 9QVO, 9QVP, 9QVQ, 9QVR, 9QVS

  • PubMed Abstract: 

    Closthioamide (CTA) is a potent antibiotic with a unique polythioamide scaffold produced by Ruminiclostridium cellulolyticum . Unlike classical non-ribosomal peptide synthetases (NRPSs), which use modular adenylation and condensation domains, CTA biosynthesis proceeds through non-canonical standalone enzymes. Central to this process is the papain-like ligase CtaG, which catalyzes amide bond formation between two distinct peptidyl carrier proteins (PCPs): CtaH, presenting para-hydroxybenzoic acid (PHBA), and CtaE, carrying a tri-β-alanine ((βAla) 3 ) chain. Using biochemical assays, chemical probes, crystallography, and mutational analysis, we show that CtaG operates via a ping-pong mechanism involving an enzyme-bound intermediate. A single substrate tunnel mediates directional transfer, enabling distal chain elongation that mirrors solid-phase peptide synthesis. Structure-based genome mining revealed homologous enzymes in the biosynthetic pathways of petrobactin, butirosin, and methylolanthanin. Together, our findings uncover a previously overlooked class of thiotemplated ligases and provide a mechanistic blueprint for engineering ribosome-independent peptide assembly lines.


  • Organizational Affiliation
    • Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07743 Jena, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Butirosin biosynthesis protein H N-terminal domain-containing protein315Ruminiclostridium cellulolyticumMutation(s): 1 
Gene Names: Ccel_3254
UniProt
Find proteins for B8I0Y7 (Ruminiclostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10))
Explore B8I0Y7 
Go to UniProtKB:  B8I0Y7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8I0Y7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.182 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.61α = 90
b = 60.28β = 108.76
c = 54.84γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XFITdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Database references