2B0Q

Crystal Structure Of 3',5"-Aminoglycoside Phosphotransferase Type IIIa ADP Neomycin B Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

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This is version 1.3 of the entry. See complete history


Literature

Substrate promiscuity of an aminoglycoside antibiotic resistance enzyme via target mimicry.

Fong, D.H.Berghuis, A.M.

(2002) EMBO J 21: 2323-2331

  • DOI: https://doi.org/10.1093/emboj/21.10.2323
  • Primary Citation of Related Structures:  
    1L8T, 2B0Q

  • PubMed Abstract: 

    The misuse of antibiotics has selected for bacteria that have evolved mechanisms for evading the effects of these drugs. For aminoglycosides, a group of clinically important bactericidal antibiotics that target the A-site of the 16S ribosomal RNA, the most common mode of resistance is enzyme-catalyzed chemical modification of the drug. While aminoglycosides are structurally diverse, a single enzyme can confer resistance to many of these antibiotics. For example, the aminoglycoside kinase APH(3')-IIIa, produced by pathogenic Gram-positive bacteria such as enterococci and staphylococci, is capable of detoxifying at least 10 distinct aminoglycosides. Here we describe the crystal structures of APH(3')-IIIa in complex with ADP and kanamycin A or neomycin B. These structures reveal that the basis for this enzyme's substrate promiscuity is the presence of two alternative subsites in the antibiotic binding pocket. Furthermore, comparison between the A-site of the bacterial ribosome and APH(3')-IIIa shows that mimicry is the second major factor in dictating the substrate spectrum of APH(3')-IIIa. These results suggest a potential strategy for drug design aimed at circumventing antibiotic resistance.


  • Organizational Affiliation

    Department of Biochemistry, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoglycoside 3'-phosphotransferase263Enterococcus faecalisMutation(s): 0 
Gene Names: aphA
EC: 2.7.1.95
UniProt
Find proteins for P0A3Y5 (Enterococcus faecalis)
Explore P0A3Y5 
Go to UniProtKB:  P0A3Y5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3Y5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NMY
Query on NMY

Download Ideal Coordinates CCD File 
B [auth A]NEOMYCIN
C23 H46 N6 O13
PGBHMTALBVVCIT-VCIWKGPPSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.357α = 90
b = 46.357β = 90
c = 301.613γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description