4H05

Crystal structure of aminoglycoside-3'-phosphotransferase of type VIII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of the novel aminoglycoside phosphotransferase AphVIII from Streptomyces rimosus with enzymatic activity modulated by phosphorylation.

Boyko, K.M.Gorbacheva, M.A.Korzhenevskiy, D.A.Alekseeva, M.G.Mavletova, D.A.Zakharevich, N.V.Elizarov, S.M.Rudakova, N.N.Danilenko, V.N.Popov, V.O.

(2016) Biochem.Biophys.Res.Commun. 477: 595-601

  • DOI: 10.1016/j.bbrc.2016.06.097

  • PubMed Abstract: 
  • Aminoglycoside phosphotransferases represent a broad class of enzymes that promote bacterial resistance to aminoglycoside antibiotics via the phosphorylation of hydroxyl groups in the latter. Here we report the spatial structure of the 3'-aminoglycos ...

    Aminoglycoside phosphotransferases represent a broad class of enzymes that promote bacterial resistance to aminoglycoside antibiotics via the phosphorylation of hydroxyl groups in the latter. Here we report the spatial structure of the 3'-aminoglycoside phosphotransferase of novel VIII class (AphVIII) solved by X-ray diffraction method with a resolution of 2.15 Å. Deep analysis of APHVIII structure and its comparison with known structures of aminoglycoside phosphotransferases of various types reveals that AphVIII has a typical two-domain fold and, however, possesses some unique characteristics that distinguish the enzyme from its known homologues. The most important difference is the presence of the activation loop with unique Ser146 residue. We demonstrate that in the apo-state of the enzyme the activation loop does not interact with other parts of the enzyme and seems to adopt catalytically competent state only after substrate binding.


    Organizational Affiliation

    Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt. 33, Bld. 2, 119071, Moscow, Russian Federation; National Research Center "Kurchatov Institute", Kurchatov Complex of NBICS-technologies, Akad. Kurchatova sqr., 1, Moscow, 123182, Russian Federation. Electronic address: kmb@inbi.ras.ru.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminoglycoside-O-phosphotransferase VIII
A, B
273Streptomyces rimosusMutation(s): 0 
Find proteins for Q9F9M5 (Streptomyces rimosus)
Go to UniProtKB:  Q9F9M5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.340α = 90.00
b = 103.340β = 94.36
c = 53.680γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
BALBESphasing
MAR345dtbdata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Data collection