8I8G

Crystal structure of Cph001-D189N in complex with CMN IIA and ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


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Literature

Discovery and characterization of genes conferring natural resistance to the antituberculosis antibiotic capreomycin.

Toh, S.I.Elaine Keisha, J.Wang, Y.L.Pan, Y.C.Jhu, Y.H.Hsiao, P.Y.Liao, W.T.Chen, P.Y.Ko, T.M.Chang, C.Y.

(2023) Commun Biol 6: 1282-1282

  • DOI: https://doi.org/10.1038/s42003-023-05681-6
  • Primary Citation of Related Structures:  
    8I80, 8I82, 8I84, 8I85, 8I86, 8I89, 8I8G, 8I8H

  • PubMed Abstract: 

    Metagenomic-based studies have predicted an extraordinary number of potential antibiotic-resistance genes (ARGs). These ARGs are hidden in various environmental bacteria and may become a latent crisis for antibiotic therapy via horizontal gene transfer. In this study, we focus on a resistance gene cph, which encodes a phosphotransferase (Cph) that confers resistance to the antituberculosis drug capreomycin (CMN). Sequence Similarity Network (SSN) analysis classified 353 Cph homologues into five major clusters, where the proteins in cluster I were found in a broad range of actinobacteria. We examine the function and antibiotics targeted by three putative resistance proteins in cluster I via biochemical and protein structural analysis. Our findings reveal that these three proteins in cluster I confer resistance to CMN, highlighting an important aspect of CMN resistance within this gene family. This study contributes towards understanding the sequence-structure-function relationships of the phosphorylation resistance genes that confer resistance to CMN.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Viomycin kinaseA [auth B],
B [auth A]
286Streptosporangium roseumMutation(s): 1 
Gene Names: Sros_4606
UniProt
Find proteins for D2B3F1 (Streptosporangium roseum (strain ATCC 12428 / DSM 43021 / JCM 3005 / NI 9100))
Explore D2B3F1 
Go to UniProtKB:  D2B3F1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2B3F1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
KBE-DPP-UAL-MYN-DPP-SERC [auth D]6Saccharothrix mutabilis subsp. capreolusMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
DPP
Query on DPP
C [auth D]L-PEPTIDE LINKINGC3 H8 N2 O2ALA
KBE
Query on KBE
C [auth D]L-PEPTIDE LINKINGC6 H14 N2 O2LYS
MYN
Query on MYN
C [auth D]L-PEPTIDE LINKINGC6 H12 N4 O2ARG
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.288α = 90
b = 87.074β = 90
c = 87.951γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan110-2113-M-A49 -026 -MY3

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release