1IUH

Crystal structure of TT0787 of thermus thermophilus HB8

Summary for 1IUH

• Entry DOI: 10.2210/pdb1iuh/pdb
• Descriptor: 2'-5' RNA Ligase (2 entities in total)
• Functional Keywords: thermus thermophilus, ligase, riken structural genomics/proteomics initiative, rsgi, structural genomics
• Biological source: Thermus thermophilus
• Total number of polymer chains: 1
• Total formula weight: 22445.91

Authors

Kato, M.,Sakai, H.,Shirouzu, M.,Kuramitsu, S.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2002-03-05, release date: 2003-06-17, Last modification date: 2023-12-27)

Primary citation

Kato, M.,Shirouzu, M.,Terada, T.,Yamaguchi, H.,Murayama, K.,Sakai, H.,Kuramitsu, S.,Yokoyama, S.
Crystal Structure of the 2'-5' RNA Ligase from Thermus thermophilus HB8
J.MOL.BIOL., 329:903-911, 2003

PubMed Abstract: The 2'-5' RNA ligase family members are bacterial and archaeal RNA ligases that ligate 5' and 3' half-tRNA molecules with 2',3'-cyclic phosphate and 5'-hydroxyl termini, respectively, to the product containing the 2'-5' phosphodiester linkage. Here, the crystal structure of the 2'-5' RNA ligase protein from an extreme thermophile, Thermus thermophilus HB8, was solved at 2.5A resolution. The structure of the 2'-5' RNA ligase superimposes well on that of the Arabidopsis thaliana cyclic phosphodiesterase (CPDase), which hydrolyzes ADP-ribose 1",2"-cyclic phosphate (a product of the tRNA splicing reaction) to the monoester ADP-ribose 1"-phosphate. Although the sequence identity between the two proteins is remarkably low (9.3%), the 2'-5' RNA ligase and CPDase structures have two HX(T/S)X motifs in their corresponding positions. The HX(T/S)X motifs play important roles in the CPDase activity, and are conserved in both the CPDases and 2'-5' RNA ligases. Therefore, the catalytic mechanism of the 2'-5' RNA ligase may be similar to that of the CPDase. On the other hand, the electrostatic potential of the cavity of the 2'-5' RNA ligase is positive, but that of the CPDase is negative. Furthermore, in the CPDase, two loops with low B-factors cover the cavity. In contrast, in the 2'-5' RNA ligase, the corresponding loops form an open conformation and are flexible. These characteristics may be due to the differences in the substrates, tRNA and ADP-ribose 1",2"-cyclic phosphate.

PubMed: 12798681
DOI: 10.1016/S0022-2836(03)00448-0

Experimental method

X-RAY DIFFRACTION (2.5 Å)