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Structural basis for the substrate recognition of aminoglycoside 7′′-phosphotransferase-Ia from Streptomyces hygroscopicus
- Source :
- Acta Crystallogr F Struct Biol Commun
- Publication Year :
- 2019
- Publisher :
- International Union of Crystallography (IUCr), 2019.
-
Abstract
- Hygromycin B (HygB) is one of the aminoglycoside antibiotics, and it is widely used as a reagent in molecular-biology experiments. Two kinases are known to inactivate HygB through phosphorylation: aminoglycoside 7′′-phosphotransferase-Ia [APH(7′′)-Ia] from Streptomyces hygroscopicus and aminoglycoside 4-phosphotransferase-Ia [APH(4)-Ia] from Escherichia coli. They phosphorylate the hydroxyl groups at positions 7′′ and 4 of the HygB molecule, respectively. Previously, the crystal structure of APH(4)-Ia was reported as a ternary complex with HygB and 5′-adenylyl-β,γ-imidodiphosphate (AMP-PNP). To investigate the differences in the substrate-recognition mechanism between APH(7′′)-Ia and APH(4)-Ia, the crystal structure of APH(7′′)-Ia complexed with HygB is reported. The overall structure of APH(7′′)-Ia is similar to those of other aminoglycoside phosphotransferases, including APH(4)-Ia, and consists of an N-terminal lobe (N-lobe) and a C-terminal lobe (C-lobe). The latter also comprises a core and a helical domain. Accordingly, the APH(7′′)-Ia and APH(4)-Ia structures fit globally when the structures are superposed at three catalytically important conserved residues, His, Asp and Asn, in the Brenner motif, which is conserved in aminoglycoside phosphotransferases as well as in eukaryotic protein kinases. On the other hand, the phosphorylated hydroxyl groups of HygB in both structures come close to the Asp residue, and the HygB molecules in each structure lie in opposite directions. These molecules were held by the helical domain in the C-lobe, which exhibited structural differences between the two kinases. Furthermore, based on the crystal structures of APH(7′′)-Ia and APH(4)-Ia, some mutated residues in their thermostable mutants reported previously were located at the same positions in the two enzymes.
- Subjects :
- Stereochemistry
Adenylyl Imidodiphosphate
Amino Acid Motifs
Mutant
Biophysics
Crystallography, X-Ray
medicine.disease_cause
Biochemistry
Catalysis
Substrate Specificity
Research Communications
Phosphotransferase
03 medical and health sciences
chemistry.chemical_compound
0302 clinical medicine
Protein Domains
Structural Biology
Escherichia coli
Genetics
medicine
Phosphorylation
Ternary complex
030304 developmental biology
0303 health sciences
Binding Sites
Kanamycin Kinase
biology
Aminoglycoside
Condensed Matter Physics
biology.organism_classification
Streptomyces
Anti-Bacterial Agents
Aminoglycosides
chemistry
030220 oncology & carcinogenesis
Hygromycin B
Streptomyces hygroscopicus
Phosphotransferases
Subjects
Details
- ISSN :
- 2053230X
- Volume :
- 75
- Database :
- OpenAIRE
- Journal :
- Acta Crystallographica Section F Structural Biology Communications
- Accession number :
- edsair.doi.dedup.....bf8864992239651d4aa4ac2707db5a9b
- Full Text :
- https://doi.org/10.1107/s2053230x19011105