2ei9
From Proteopedia
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| - | [[Image:2ei9.jpg|left|200px]] | + | [[Image:2ei9.jpg|left|200px]] |
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| - | '''Crystal structure of R1Bm endonuclease domain''' | + | {{Structure |
| + | |PDB= 2ei9 |SIZE=350|CAPTION= <scene name='initialview01'>2ei9</scene>, resolution 2.Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=ACY:ACETIC ACID'>ACY</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
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| + | '''Crystal structure of R1Bm endonuclease domain''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2EI9 is a [ | + | 2EI9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bombyx_mori Bombyx mori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EI9 OCA]. |
==Reference== | ==Reference== | ||
| - | Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies., Maita N, Aoyagi H, Osanai M, Shirakawa M, Fujiwara H, Nucleic Acids Res. 2007;35(12):3918-27. Epub 2007 May 30. PMID:[http:// | + | Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies., Maita N, Aoyagi H, Osanai M, Shirakawa M, Fujiwara H, Nucleic Acids Res. 2007;35(12):3918-27. Epub 2007 May 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17537809 17537809] |
[[Category: Bombyx mori]] | [[Category: Bombyx mori]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: four layered alpha beta sandwich]] | [[Category: four layered alpha beta sandwich]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:40:36 2008'' |
Revision as of 14:40, 20 March 2008
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of R1Bm endonuclease domain
Overview
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.
About this Structure
2EI9 is a Single protein structure of sequence from Bombyx mori. Full crystallographic information is available from OCA.
Reference
Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies., Maita N, Aoyagi H, Osanai M, Shirakawa M, Fujiwara H, Nucleic Acids Res. 2007;35(12):3918-27. Epub 2007 May 30. PMID:17537809
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