1VGJ

Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii

Summary for 1VGJ

• Entry DOI: 10.2210/pdb1vgj/pdb
• Descriptor: Hypothetical protein PH0099 (2 entities in total)
• Functional Keywords: alpha+beta, ligt-like, structural genomics, ligase
• Biological source: Pyrococcus horikoshii
• Total number of polymer chains: 1
• Total formula weight: 21271.25

Authors

Yao, M.,Morita, H.,Okada, A.,Tanaka, I. (deposition date: 2004-04-27, release date: 2005-06-07, Last modification date: 2024-11-13)

Primary citation

Gao, Y.G.,Yao, M.,Okada, A.,Tanaka, I.
The structure of Pyrococcus horikoshii 2'-5' RNA ligase at 1.94 A resolution reveals a possible open form with a wider active-site cleft
ACTA CRYSTALLOGR.,SECT.F, 62:1196-1200, 2006

PubMed Abstract: Bacterial and archaeal 2'-5' RNA ligases, members of the 2H phosphoesterase superfamily, catalyze the linkage of the 5' and 3' exons via a 2'-5'-phosphodiester bond during tRNA-precursor splicing. The crystal structure of the 2'-5' RNA ligase PH0099 from Pyrococcus horikoshii OT3 was solved at 1.94 A resolution (PDB code 1vgj). The molecule has a bilobal alpha+beta arrangement with two antiparallel beta-sheets constituting a V-shaped active-site cleft, as found in other members of the 2H phosphoesterase superfamily. The present structure was significantly different from that determined previously at 2.4 A resolution (PDB code 1vdx) in the active-site cleft; the entrance to the cleft is wider and the active site is easily accessible to the substrate (RNA precursor) in our structure. Structural comparison with the 2'-5' RNA ligase from Thermus thermophilus HB8 also revealed differences in the RNA precursor-binding region. The structural differences in the active-site residues (tetrapeptide motifs H-X-T/S-X) between the members of the 2H phosphoesterase superfamily are discussed.

PubMed: 17142895
DOI: 10.1107/S1744309106046616

Experimental method

X-RAY DIFFRACTION (1.94 Å)