7ZHE

Crystal structure of CtaZ from Ruminiclostridium cellulolyticum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Specialized Polythioamide-Binding Protein Confers Antibiotic Self-Resistance in Anaerobic Bacteria.

Gude, F.Molloy, E.M.Horch, T.Dell, M.Dunbar, K.L.Krabbe, J.Groll, M.Hertweck, C.

(2022) Angew Chem Int Ed Engl 61: e202206168-e202206168

  • DOI: https://doi.org/10.1002/anie.202206168
  • Primary Citation of Related Structures:  
    7ZHD, 7ZHE

  • PubMed Abstract: 

    Understanding antibiotic resistance mechanisms is central to the development of anti-infective therapies and genomics-based drug discovery. Yet, many knowledge gaps remain regarding the resistance strategies employed against novel types of antibiotics from less-explored producers such as anaerobic bacteria, among them the Clostridia. Through the use of genome editing and functional assays, we found that CtaZ confers self-resistance against the copper chelator and gyrase inhibitor closthioamide (CTA) in Ruminiclostridium cellulolyticum. Bioinformatics, biochemical analyses, and X-ray crystallography revealed CtaZ as a founding member of a new group of GyrI-like proteins. CtaZ is unique in binding a polythioamide scaffold in a ligand-optimized hydrophobic pocket, thereby confining CTA. By genome mining using CtaZ as a handle, we discovered previously overlooked homologs encoded by diverse members of the phylum Firmicutes, including many pathogens. In addition to characterizing both a new role for a GyrI-like domain in self-resistance and unprecedented thioamide binding, this work aids in uncovering related drug-resistance mechanisms.


  • Organizational Affiliation

    Research Unit Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745, Jena, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription activator effector binding158Ruminiclostridium cellulolyticumMutation(s): 0 
Gene Names: Ccel_3263
UniProt
Find proteins for B8I0Z6 (Ruminiclostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10))
Explore B8I0Z6 
Go to UniProtKB:  B8I0Z6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8I0Z6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.34α = 90
b = 121.34β = 90
c = 108.4γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Communitys Seventh Framework ProgrammeEuropean Union283570

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description