5y9a

Crystal structure of the complex of peptidyl tRNA hydrolase with a phosphate ion at the substrate binding site and cytarabine at a new ligand binding site at 1.1 A resolution

spinqualitylabelsall models 5y9a, resolution 1.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5y9a is a 1 chain structure with sequence from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841. This structure supersedes the now removed PDB entry 4lwr. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.1Å Ligands: AR3, PO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function D0C9L6_ACIB2 The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.[HAMAP-Rule:MF_00083] Publication Abstract from PubMed Peptidyl-tRNA hydrolase (Pth) catalyzes the breakdown of peptidyl-tRNA into peptide and tRNA components. Pth from Acinetobacter baumannii (AbPth) was cloned, expressed, purified and crystallized in a native unbound (AbPth-N) state and in a bound state with the phosphate ion and cytosine arabinoside (cytarabine) (AbPth-C). Structures of AbPth-N and AbPth-C were determined at 1.36 and 1.10 A resolutions, respectively. The structure of AbPth-N showed that the active site is filled with water molecules. In the structure of AbPth-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 AbPth-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 (KD) of 3.3 +/- 0.8 x 10(-7) M for cytarabine. The binding studies using surface plasmon resonance gave a KD value of 3.7 +/- 0.7 x 10(-7) 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. Search of multiple hot spots on the surface of peptidyl-tRNA hydrolase: structural, binding and antibacterial studies.,Kaushik S, Iqbal N, Singh N, Sikarwar JS, Singh PK, Sharma P, Kaur P, Sharma S, Owais M, Singh TP Biochem J. 2018 Feb 9;475(3):547-560. doi: 10.1042/BCJ20170666. PMID:29301982 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Peptidyl-tRNA hydrolase

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