7F0F

Crystal structure of capreomycin phosphotransferase in complex with CMN IIB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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

Dual-Mechanism Confers Self-Resistance to the Antituberculosis Antibiotic Capreomycin.

Pan, Y.C.Wang, Y.L.Toh, S.I.Hsu, N.S.Lin, K.H.Xu, Z.Huang, S.C.Wu, T.K.Li, T.L.Chang, C.Y.

(2022) ACS Chem Biol 17: 138-146

  • DOI: https://doi.org/10.1021/acschembio.1c00799
  • Primary Citation of Related Structures:  
    7F0A, 7F0B, 7F0C, 7F0F

  • PubMed Abstract: 

    Capreomycin (CMN) is an important second-line antituberculosis antibiotic isolated from Saccharothrix mutabilis subspecies capreolus . The gene cluster for CMN biosynthesis has been identified and sequenced, wherein the cph gene was annotated as a phosphotransferase likely engaging in self-resistance. Previous studies reported that Cph inactivates two CMNs, CMN IA and IIA, by phosphorylation. We, herein, report that (1) Escherichia coli harboring the cph gene becomes resistant to both CMN IIA and IIB, (2) phylogenetic analysis regroups Cph to a new clade in the phosphotransferase protein family, (3) Cph shares a three-dimensional structure akin to the aminoglycoside phosphotransferases with a high binding affinity ( K D ) to both CMN IIA and IIB at micromolar levels, and (4) Cph utilizes either ATP or GTP as a phosphate group donor transferring its γ-phosphate to the hydroxyl group of CMN IIA. Until now, Cph and Vph (viomycin phosphotransferase) are the only two known enzymes inactivating peptide-based antibiotics through phosphorylation. Our biochemical characterization and structural determination conclude that Cph confers the gene-carrying species resistance to CMN by means of either chemical modification or physical sequestration, a naturally manifested belt and braces strategy. These findings add a new chapter into the self-resistance of bioactive natural products, which is often overlooked while designing new bioactive molecules.


  • Organizational Affiliation

    Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010 Taiwan, R.O.C.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capreomycin phosphotransferase294Saccharothrix mutabilis subsp. capreolusMutation(s): 0 
Gene Names: cph
UniProt
Find proteins for Q53826 (Saccharothrix mutabilis subsp. capreolus)
Explore Q53826 
Go to UniProtKB:  Q53826
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53826
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DPP-ALA-DPP-UAL-MYN-KBEB [auth C]6Saccharothrix mutabilis subsp. capreolusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
DPP
Query on DPP
B [auth C]L-PEPTIDE LINKINGC3 H8 N2 O2ALA
KBE
Query on KBE
B [auth C]L-PEPTIDE LINKINGC6 H14 N2 O2LYS
MYN
Query on MYN
B [auth C]L-PEPTIDE LINKINGC6 H12 N4 O2ARG
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.101α = 90
b = 92.101β = 90
c = 119.006γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan107-2113-M-009-021-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description