› 5iqi

X-ray diffraction
2.15Å resolution

Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) Y237F mutant in complex with GMPPNP and Magnesium

Released:
DOI: 10.2210/pdb5iqi/pdb
PDB entry 5iqi coloured by chain, front view.
PDB entry 5iqi coloured by chain, side view.
PDB entry 5iqi 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: 35.93 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

3 bound ligands:
Ligand GNP 4 x GNP
Ligand MG 8 x MG
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 90.169Å b: 99.74Å c: 92.97Å
α: 90° β: 105.1° γ: 90°
R-values:
R R work R free
0.17 0.167 0.211
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