6IY9

Crystal structure of aminoglycoside 7"-phoshotransferase-Ia (APH(7")-Ia/HYG) from Streptomyces hygroscopicus complexed with hygromycin B

Summary for 6IY9

• Entry DOI: 10.2210/pdb6iy9/pdb
• Descriptor: Hygromycin-B 7''-O-kinase, HYGROMYCIN B VARIANT, 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID, ... (5 entities in total)
• Functional Keywords: kinase, complex, transferase
• Biological source: Streptomyces hygroscopicus
• Total number of polymer chains: 2
• Total formula weight: 78432.47

Authors

Takenoya, M.,Shimamura, T.,Yamanaka, R.,Adachi, Y.,Ito, S.,Sasaki, Y.,Nakamura, A.,Yajima, S. (deposition date: 2018-12-14, release date: 2019-09-11, Last modification date: 2024-10-23)

Primary citation

Takenoya, M.,Shimamura, T.,Yamanaka, R.,Adachi, Y.,Ito, S.,Sasaki, Y.,Nakamura, A.,Yajima, S.
Structural basis for the substrate recognition of aminoglycoside 7''-phosphotransferase-Ia from Streptomyces hygroscopicus.
Acta Crystallogr.,Sect.F, 75:599-607, 2019

PubMed 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.

PubMed: 31475927
DOI: 10.1107/S2053230X19011105

Experimental method

X-RAY DIFFRACTION (2.4 Å)