9QVR | pdb_00009qvr

Crystal structure of the CtaG_H128A variant from Ruminiclostridium cellulolyticum in complex with PHBA (P2(1)2(1)2(1)-medium)

• PDB DOI: https://doi.org/10.2210/pdb9QVR/pdb

• Classification: LIGASE
• Organism(s): Ruminiclostridium cellulolyticum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-04-11 Released: 2025-10-01 
• Deposition Author(s): Gude, F., Bohne, A., Dell, M., Franke, J., Dunbar, K.L., Groll, M., Hertweck, C.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

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

• PubMed: 41641319 
• DOI: https://doi.org/10.1016/j.chempr.2025.102740
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07743 Jena, Germany.
Center for Protein Assemblies, Department Bioscience, School of Natural Sciences, Technical University Munich, Garching, Germany.
Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany.
Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.59 kDa 
• Atom Count: 5,377 
• Modeled Residue Count: 612 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Butirosin biosynthesis protein H N-terminal domain-containing protein	A, B	315	Ruminiclostridium cellulolyticum	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HBA (Subject of Investigation/LOI)	C [auth A], E [auth B]	P-HYDROXYBENZALDEHYDE C7 H6 O2 RGHHSNMVTDWUBI-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.69	α = 90
b = 99.67	β = 90
c = 100.74	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Gude, F., Bohne, A., Dell, M., Franke, J., Dunbar, K.L., Groll, M., Hertweck, C.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History  

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