4FEW

Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor pyrazolopyrimidine PP2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance.

Stogios, P.J., Spanogiannopoulos, P., Evdokimova, E., Egorova, O., Shakya, T., Todorovic, N., Capretta, A., Wright, G.D., Savchenko, A.

(2013) Biochem J 454: 191-200

  • DOI: 10.1042/BJ20130317
  • Primary Citation of Related Structures:  
    4EJ7, 4FEU, 4FEV, 4FEW, 4FEX, 4GKH, 4GKI

  • PubMed Abstract: 

    • Activity of the aminoglycoside phosphotransferase APH(3')-Ia leads to resistance to aminoglycoside antibiotics in pathogenic Gram-negative bacteria, and contributes to the clinical obsolescence of this class of antibiotics. One strategy to rescue compromised antibiotics such as aminoglycosides is targeting the enzymes that confer resistance with small molecules ...

    Activity of the aminoglycoside phosphotransferase APH(3')-Ia leads to resistance to aminoglycoside antibiotics in pathogenic Gram-negative bacteria, and contributes to the clinical obsolescence of this class of antibiotics. One strategy to rescue compromised antibiotics such as aminoglycosides is targeting the enzymes that confer resistance with small molecules. We demonstrated previously that ePK (eukaryotic protein kinase) inhibitors could inhibit APH enzymes, owing to the structural similarity between these two enzyme families. However, limited structural information of enzyme-inhibitor complexes hindered interpretation of the results. In addition, cross-reactivity of compounds between APHs and ePKs represents an obstacle to their use as aminoglycoside adjuvants to rescue aminoglycoside antibiotic activity. In the present study, we structurally and functionally characterize inhibition of APH(3')-Ia by three diverse chemical scaffolds, anthrapyrazolone, 4-anilinoquinazoline and PP (pyrazolopyrimidine), and reveal distinctions in the binding mode of anthrapyrazolone and PP compounds to APH(3')-Ia compared with ePKs. Using this observation, we identify PP derivatives that select against ePKs, attenuate APH(3')-Ia activity and rescue aminoglycoside antibiotic activity against a resistant Escherichia coli strain. The structures described in the present paper and the inhibition studies provide an important opportunity for structure-based design of compounds to target aminoglycoside phosphotransferases for inhibition, potentially overcoming this form of antibiotic resistance.

    Organizational Affiliation: 

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aminoglycoside 3'-phosphotransferase AphA1-IAB
A, B, C, D, E, F
A, B, C, D, E, F
272Acinetobacter baumannii AYEMutation(s): 0 
Gene Names: ABAYE3578, APHA1-IAB
EC: 2.7.1.95
UniProt
Find proteins for B0VD92 (Acinetobacter baumannii (strain AYE))
Explore B0VD92 
Go to UniProtKB:  B0VD92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0VD92
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KAN
Query on KAN
Download Ideal Coordinates CCD File 
CA [auth F],
G [auth A],
L [auth B],
P [auth C],
S [auth D],
CA [auth F],
G [auth A],
L [auth B],
P [auth C],
S [auth D],
Y [auth E]
KANAMYCIN A
C18 H36 N4 O11
SBUJHOSQTJFQJX-NOAMYHISSA-N		 Ligand Interaction
PP2
Query on PP2
Download Ideal Coordinates CCD File 
DA [auth F],
H [auth A],
M [auth B],
Q [auth C],
T [auth D],
DA [auth F],
H [auth A],
M [auth B],
Q [auth C],
T [auth D],
Z [auth E]
1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE
C15 H17 Cl N5
PBBRWFOVCUAONR-UHFFFAOYSA-O		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
HA [auth F],
R [auth C]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
BA [auth E],
GA [auth F],
K [auth A],
O [auth B],
W [auth D],
BA [auth E],
GA [auth F],
K [auth A],
O [auth B],
W [auth D],
X [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
AA [auth E],
EA [auth F],
FA [auth F],
I [auth A],
N [auth B],
AA [auth E],
EA [auth F],
FA [auth F],
I [auth A],
N [auth B],
U [auth D],
V [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
PP2 PDBBind:  4FEW Ki: 6200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 
  • Space Group: P 1
  • Diffraction Data DOI: 10.18430/M34FEW
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.28α = 61.22
b = 93.579β = 73.18
c = 96.399γ = 87.35
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references
  • Version 1.2: 2013-08-07
    Changes: Database references
  • Version 1.3: 2013-09-04
    Changes: Database references