Structure of IDP92558

Crystal structure of aminoglycoside nucleotidylyltransferase ANT(2")-Ia, apo form

Edit deposit information
CSGID target
IDP92558 
PDB Id
4WQK (NCBI MMDB
Authors
G.Cox,P.J.Stogios,A.Savchenko,G.D.Wright,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Peter Stogios 
Responsible lab
University of Calgary 
Deposition Date
Oct 22, 2014 
Release Date
Nov 12, 2014 

Annotation

Description
The aminoglycosides are highly effective broad-spectrum antimicrobial agents. However, their efficacy is diminished due to enzyme mediated covalent modification, which reduces affinity of the drug for the target ribosome. One of the most prevalent aminoglycoside resistance enzymes in Gram-negative pathogens is the adenylyltransferase ANT(2”)-Ia, which confers resistance to gentamicin, tobramycin and kanamycin. Despite the importance of this enzyme in drug resistance, its structure and molecular mechanism have been elusive. This study describes the structural and mechanistic basis for adenylylation of aminoglycosides by the ANT(2’’)-Ia enzyme. ANT(2”)-Ia confers resistance by magnesium-dependent transfer of nucleoside monophosphate (AMP) to the 2”-hydroxyl of aminoglycoside substrates containing a 2-deoxystreptamine core. The catalyzed reaction follows a direct AMP transfer mechanism from ATP to the substrate antibiotic. Central to catalysis is the coordination of two Mg2+ ions, positioning of the modifiable substrate ring and presence of a catalytic base (Asp86). Comparative structural analysis revealed that ANT(2’’)-Ia has a two-domain structure with an N-terminal active site architecture that is conserved amongst other antibiotic nucleotidyltransferases including Lnu(A), LinB, ANT(4’)-Ia, ANT(4”)-Ib and ANT(6)-Ia. There is also similarity between the nucleotidyltransferase fold of ANT(2”)-Ia and DNA polymerase β. This similarity is consistent with evolution from a common ancestor, with the nucleotidyltransferase fold having adapted for activity against chemically-distinct molecules. 
Functional assignment
antibiotic resistance 

Ligands

Ligand code Name Ligand type
CL crystallization
IPA crystallization
GOL crystallization
MG biological

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=45.53Å, b=42.11Å, c=47.70Å
α=90.00, β=105.49, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
37.07-1.48Å (1.52-1.48Å)  
Rall(%)
16.1 
Rwork(%)
15.9 (28.3) 
Rfree(%)
19.6 (32.1) 
Num. observed reflections
30063 (1517) 
Num. Rfree reflections
2137 (118) 
Completeness(%)
96.3 (78.0) 

Model parameters

Num Atoms
1415  
Num Waters
262  
Num Hetatoms
329  
Model mean isotropic B factor
27.520Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.441°  
RMSD dihedral angle
12.91°
 
Filename uploaded
4WQK.pdb (uploaded on Nov 13, 2014 2:01 PM)  
Inserted
Nov 12, 2014