5Y98

Crystal structure of native unbound peptidyl tRNA hydrolase from Acinetobacter baumannii at 1.36 A resolution

Replaces:  3WH4

Summary for 5Y98

• Entry DOI: 10.2210/pdb5y98/pdb
• Descriptor: Peptidyl-tRNA hydrolase, GLYCEROL (3 entities in total)
• Functional Keywords: hydrolase
• Biological source: Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)
• Total number of polymer chains: 1
• Total formula weight: 21342.33

Authors

Iqbal, N.,Singh, N.,Kaushik, S.,Singh, P.K.,Sharma, S.,Singh, T.P. (deposition date: 2017-08-23, release date: 2017-09-13, Last modification date: 2023-11-22)

Primary citation

Kaushik, S.,Iqbal, N.,Singh, N.,Sikarwar, J.S.,Singh, P.K.,Sharma, P.,Kaur, P.,Sharma, S.,Owais, M.,Singh, T.P.
Search of multiple hot spots on the surface of peptidyl-tRNA hydrolase: structural, binding and antibacterial studies.
Biochem. J., 475:547-560, 2018

PubMed Abstract: Peptidyl-tRNA hydrolase (Pth) catalyzes the breakdown of peptidyl-tRNA into peptide and tRNA components. Pth from (Pth) was cloned, expressed, purified and crystallized in a native unbound (Pth-N) state and in a bound state with the phosphate ion and cytosine arabinoside (cytarabine) (Pth-C). Structures of Pth-N and Pth-C were determined at 1.36 and 1.10 Å resolutions, respectively. The structure of Pth-N showed that the active site is filled with water molecules. In the structure of Pth-C, a phosphate ion is present in the active site, while cytarabine is bound in a cleft which is located away from the catalytic site. The cytarabine-binding site is formed with residues: Gln19, Trp27, Glu30, Gln31, Lys152, Gln158 and Asp162. In the structure of Pth-N, the side chains of two active-site residues, Asn70 and Asn116, were observed in two conformations. Upon binding of the phosphate ion in the active site, the side chains of both residues were ordered to single conformations. Since Trp27 is present at the cytarabine-binding site, the fluorescence studies were carried out which gave a dissociation constant () of 3.3 ± 0.8 × 10 M for cytarabine. The binding studies using surface plasmon resonance gave a value of 3.7 ± 0.7 × 10 M. The bacterial inhibition studies using the agar diffusion method and the biofilm inhibition assay established the strong antimicrobial potential of cytarabine. It also indicated that cytarabine inhibited Gram-negative bacteria more profoundly when compared with Gram-positive bacteria in a dose-dependent manner. Cytarabine was also effective against the drug-resistant bacteria both alone as well as in combination with other antibiotics.

PubMed: 29301982
DOI: 10.1042/BCJ20170666

Experimental method

X-RAY DIFFRACTION (1.36 Å)