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 
  • R-Value Observed: 0.198 

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This is version 1.3 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: https://doi.org/10.1016/j.bbrc.2016.06.097
  • Primary Citation of Related Structures:  
    4H05

  • 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'-aminoglycoside phosphotransferase of novel VIII class (AphVIII) solved by X-ray diffraction method with a resolution of 2 ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aminoglycoside-O-phosphotransferase VIII
A, B
273Streptomyces rimosusMutation(s): 0 
Gene Names: AAG11411
EC: 2.7.1.95
UniProt
Find proteins for Q9F9M5 (Streptomyces rimosus)
Explore Q9F9M5 
Go to UniProtKB:  Q9F9M5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F9M5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.34α = 90
b = 103.34β = 94.36
c = 53.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
BALBESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Data collection
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description