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 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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
EC: 2.7.1.103
UniProt
Find proteins for D2B3F1 (Streptosporangium roseum (strain ATCC 12428 / DSM 43021 / JCM 3005 / KCTC 9067 / NCIMB 10171 / NRRL 2505 / NI 9100))
Explore D2B3F1 
Go to UniProtKB:  D2B3F1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2B3F1
Sequence Annotations
Expand
  • 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

View Full Validation Report



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