2EI9

Crystal structure of R1Bm endonuclease domain

Summary for 2EI9

• Entry DOI: 10.2210/pdb2ei9/pdb
• Descriptor: Non-LTR retrotransposon R1Bmks ORF2 protein, ACETIC ACID (3 entities in total)
• Functional Keywords: four layered alpha beta sandwich, gene regulation
• Biological source: Bombyx mori (domestic silkworm)
• Total number of polymer chains: 1
• Total formula weight: 26777.14

Authors

Maita, N.,Aoyagi, H.,Osanai, M.,Shirakawa, M.,Fujiwara, H. (deposition date: 2007-03-12, release date: 2007-07-17, Last modification date: 2023-10-25)

Primary citation

Maita, N.,Aoyagi, H.,Osanai, M.,Shirakawa, M.,Fujiwara, H.
Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies.
Nucleic Acids Res., 35:3918-3927, 2007

PubMed Abstract: R1Bm is a long interspersed element (LINE) inserted into a specific sequence within 28S rDNA of the silkworm genome. Of two open reading frames (ORFs) of R1Bm, ORF2 encodes a reverse transcriptase (RT) and an endonuclease (EN) domain which digests specifically both top and bottom strand of the target sequence in 28S rDNA. To elucidate the sequence specificity of EN domain of R1Bm (R1Bm EN), we examined the cleavage tendency for the target sequences, and found that 5'-A(G/C)(A/T)!(A/G)T-3' is the consensus sequence (! = cleavage site). We also determined the crystal structure of R1Bm EN at 2.0 A resolution. Its structure was basically similar to AP endonuclease family, but had a special beta-hairpin at the edge of the DNA binding surface, which is a common feature among EN of LINEs. Point-mutations on the DNA binding surface of R1Bm EN significantly decreased the cleavage activities, but did not affect the sequence recognition in most residues. However, two mutants Y98A and N180A had altered cleavage patterns, suggesting an important role of these residues (Y98 and N180) for the sequence recognition of R1Bm EN. In addition, Y98A mutant showed another cleavage pattern, that implies de novo design of novel sequence-specific EN.

PubMed: 17537809
DOI: 10.1093/nar/gkm397

Experimental method

X-RAY DIFFRACTION (2 Å)