1UDN

Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus

Summary for 1UDN

• Entry DOI: 10.2210/pdb1udn/pdb
• Related: 1UDO 1UDQ 1UDS
• Descriptor: Ribonuclease PH, PHOSPHATE ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: transferase, riken structural genomics/proteomics initiative, rsgi, structural genomics
• Biological source: Aquifex aeolicus
• Total number of polymer chains: 1
• Total formula weight: 28695.55

Authors

Ishii, R.,Nureki, O.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2003-05-02, release date: 2003-09-23, Last modification date: 2023-12-27)

Primary citation

Ishii, R.,Nureki, O.,Yokoyama, S.
Crystal Structure of the tRNA Processing Enzyme RNase PH from Aquifex aeolicus
J.Biol.Chem., 278:32397-32404, 2003

PubMed Abstract: RNase PH is one of the exoribonucleases that catalyze the 3' end processing of tRNA in bacteria. RNase PH removes nucleotides following the CCA sequence of tRNA precursors by phosphorolysis and generates mature tRNAs with amino acid acceptor activity. In this study, we determined the crystal structure of Aquifex aeolicus RNase PH bound with a phosphate, a co-substrate, in the active site at 2.3-A resolution. RNase PH has the typical alpha/beta fold, which forms a hexameric ring structure as a trimer of dimers. This ring structure resembles that of the polynucleotide phosphorylase core domain homotrimer, another phosphorolytic exoribonuclease. Four amino acid residues, Arg-86, Gly-124, Thr-125, and Arg-126, of RNase PH are involved in the phosphate-binding site. Mutational analyses of these residues showed their importance in the phosphorolysis reaction. A docking model with the tRNA acceptor stem suggests how RNase PH accommodates substrate RNAs.

PubMed: 12746447
DOI: 10.1074/jbc.M300639200

Experimental method

X-RAY DIFFRACTION (2.3 Å)