1XTY

Crystal structure of Sulfolobus solfataricus peptidyl-tRNA hydrolase

Summary for 1XTY

• Entry DOI: 10.2210/pdb1xty/pdb
• Descriptor: Peptidyl-tRNA hydrolase, SULFATE ION (3 entities in total)
• Functional Keywords: mixed beta sheet, hydrolase
• Biological source: Sulfolobus solfataricus
• Cellular location: Cytoplasm: Q980V1
• Total number of polymer chains: 4
• Total formula weight: 53390.46

Authors

Fromant, M.,Schmitt, E.,Mechulam, Y.,Lazennec, C.,Plateau, P.,Blanquet, S. (deposition date: 2004-10-25, release date: 2005-03-22, Last modification date: 2024-03-13)

Primary citation

Fromant, M.,Schmitt, E.,Mechulam, Y.,Lazennec, C.,Plateau, P.,Blanquet, S.
Crystal structure at 1.8 A resolution and identification of active site residues of Sulfolobus solfataricus peptidyl-tRNA hydrolase.
Biochemistry, 44:4294-4301, 2005

PubMed Abstract: The 3-D structure of the peptidyl-tRNA hydrolase from the archaea Sulfolobus solfataricus has been solved at 1.8 A resolution. Homologues of this enzyme are found in archaea and eucarya. Bacteria display a different type of peptidyl-tRNA hydrolase that is also encountered in eucarya. In solution, the S. solfataricus hydrolase behaves as a dimer. In agreement, the crystalline structure of this enzyme indicates the formation of a dimer. Each protomer is made of a mixed five-stranded beta-sheet surrounded by two groups of two alpha-helices. The dimer interface is mainly formed by van der Waals interactions between hydrophobic residues belonging to the two N-terminal alpha1 helices contributed by two protomers. Site-directed mutagenesis experiments were designed for probing the basis of specificity of the archaeal hydrolase. Among the strictly conserved residues within the archaeal/eucaryal peptidyl-tRNA hydrolase family, three residues, K18, D86, and T90, appear of utmost importance for activity. They are located in the N-part of alpha1 and in the beta3-beta4 loop. K18 and D86, which form a salt bridge, might play a role in the catalysis thanks to their acid and basic functions, whereas the OH group of T90 could act as a nucleophile. These observations clearly distinguish the active site of the archaeal/eucaryal hydrolases from that of the bacterial/eucaryal ones, where a histidine is believed to serve as the catalytic base.

PubMed: 15766258
DOI: 10.1021/bi047711k

Experimental method

X-RAY DIFFRACTION (1.8 Å)