› 5iqe

X-ray diffraction
2.5Å resolution

Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) in complex with GMPPNP, Magnesium, and Neomycin B

Released:
DOI: 10.2210/pdb5iqe/pdb
PDB entry 5iqe coloured by chain, front view.
PDB entry 5iqe coloured by chain, side view.
PDB entry 5iqe coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2″)-Ia.
Caldwell SJ, Huang Y, Berghuis AM
Structure 24 935-45 (2016)
PMID: 27161980

Function and Biology Details

Reaction catalysed: 
GTP + gentamicin = GDP + gentamicin 2''-phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140902 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional AAC/APH Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 305 amino acids
Theoretical weight: 35.95 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A0C1 (Residues: 175-479; Coverage: 64%)
Gene names: R015, VRA0030, aacA-aphD
Sequence domains: Phosphotransferase enzyme family
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand GNP 4 x GNP
Ligand NMY 4 x NMY
Ligand MG 8 x MG
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P21
Unit cell:
a: 90.18Å b: 100.36Å c: 93.94Å
α: 90° β: 105.3° γ: 90°
R-values:
R R work R free
0.171 0.169 0.214
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Amikacin: Uses, Resistance, and Prospects for Inhibition.
Ramirez et al. (2017)
1 more

3 mentions without citation

Surface plasmon resonance and molecular docking studies of bovine serum albumin interaction with neomycin: kinetic and thermodynamic analysis.
Sharifi et al. (2017)
2 more