6IY9

Crystal structure of aminoglycoside 7"-phoshotransferase-Ia (APH(7")-Ia/HYG) from Streptomyces hygroscopicus complexed with hygromycin B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis for the substrate recognition of aminoglycoside 7''-phosphotransferase-Ia from Streptomyces hygroscopicus.

Takenoya, M.Shimamura, T.Yamanaka, R.Adachi, Y.Ito, S.Sasaki, Y.Nakamura, A.Yajima, S.

(2019) Acta Crystallogr F Struct Biol Commun 75: 599-607

  • DOI: https://doi.org/10.1107/S2053230X19011105
  • Primary Citation of Related Structures:  
    6IY9

  • PubMed Abstract: 

    Hygromycin B (HygB) is one of the aminoglycoside antibiotics, and it is widely used as a reagent in molecular-biology experiments. Two kinases are known to inactivate HygB through phosphorylation: aminoglycoside 7''-phosphotransferase-Ia [APH(7'')-Ia] from Streptomyces hygroscopicus and aminoglycoside 4-phosphotransferase-Ia [APH(4)-Ia] from Escherichia coli. They phosphorylate the hydroxyl groups at positions 7'' and 4 of the HygB molecule, respectively. Previously, the crystal structure of APH(4)-Ia was reported as a ternary complex with HygB and 5'-adenylyl-β,γ-imidodiphosphate (AMP-PNP). To investigate the differences in the substrate-recognition mechanism between APH(7'')-Ia and APH(4)-Ia, the crystal structure of APH(7'')-Ia complexed with HygB is reported. The overall structure of APH(7'')-Ia is similar to those of other aminoglycoside phosphotransferases, including APH(4)-Ia, and consists of an N-terminal lobe (N-lobe) and a C-terminal lobe (C-lobe). The latter also comprises a core and a helical domain. Accordingly, the APH(7'')-Ia and APH(4)-Ia structures fit globally when the structures are superposed at three catalytically important conserved residues, His, Asp and Asn, in the Brenner motif, which is conserved in aminoglycoside phosphotransferases as well as in eukaryotic protein kinases. On the other hand, the phosphorylated hydroxyl groups of HygB in both structures come close to the Asp residue, and the HygB molecules in each structure lie in opposite directions. These molecules were held by the helical domain in the C-lobe, which exhibited structural differences between the two kinases. Furthermore, based on the crystal structures of APH(7'')-Ia and APH(4)-Ia, some mutated residues in their thermostable mutants reported previously were located at the same positions in the two enzymes.


  • Organizational Affiliation

    Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hygromycin-B 7''-O-kinase
A, B
340Streptomyces hygroscopicusMutation(s): 1 
Gene Names: hyg
EC: 2.7.1.119
UniProt
Find proteins for P09979 (Streptomyces hygroscopicus)
Explore P09979 
Go to UniProtKB:  P09979
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09979
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.59α = 90
b = 151.59β = 90
c = 151.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references