5ZEG

Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site

  • Classification: RNA
  • Organism(s): synthetic construct

  • Deposited: 2018-02-27 Released: 2018-03-21 
  • Deposition Author(s): Kanazawa, H., Baba, F., Koganei, M., Kondo, J.
  • Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan); Kurata Grant; Ichiro Kanehara Foundation; Japan Science Society 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.

Kanazawa, H.Baba, F.Koganei, M.Kondo, J.

(2017) Nucleic Acids Res. 45: 12529-12535

  • DOI: 10.1093/nar/gkx882
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The aminoglycoside resistance conferred by an N1-methylation of A1408 in 16S rRNA by a novel plasmid-mediated methyltransferase NpmA can be a future health threat. In the present study, we have determined crystal structures of the bacterial ribosomal ...

    The aminoglycoside resistance conferred by an N1-methylation of A1408 in 16S rRNA by a novel plasmid-mediated methyltransferase NpmA can be a future health threat. In the present study, we have determined crystal structures of the bacterial ribosomal decoding A site with an A1408m1A antibiotic-resistance mutation both in the presence and absence of aminoglycosides. G418 and paromomycin both possessing a 6'-OH group specifically bind to the mutant A site and disturb its function as a molecular switch in the decoding process. On the other hand, binding of gentamicin with a 6'-NH3+ group to the mutant A site could not be observed in the present crystal structure. These observations agree with the minimum inhibitory concentration of aminoglycosides against Escherichia coli. In addition, one of our crystal structures suggests a possible conformational change of A1408 during the N1-methylation reaction by NpmA. The structural information obtained explains how bacteria acquire resistance against aminoglycosides along with a minimum of fitness cost by the N1-methylation of A1408 and provides novel information for designing the next-generation aminoglycoside.


    Organizational Affiliation

    Graduate School of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')A,B,C23synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
1MA
Query on 1MA
A, B, C
RNA LINKINGC11 H16 N5 O7 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 159.700α = 90.00
b = 46.520β = 96.35
c = 38.760γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
PHENIXrefinement
PHASERphasing
Cootmodel building
d*TREKdata scaling
d*TREKdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan23790054
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan26860025
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17K08248
Kurata GrantJapan2013- 20
Ichiro Kanehara FoundationJapan15KI192
Japan Science SocietyJapan28-325
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17K08248

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release