3c0w

From Proteopedia

I-SceI in complex with a bottom nicked DNA substrate

PDB ID 3c0w

Drag the structure with the mouse to rotate

Structural highlights

3c0w is a 4 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SCE1_YEAST Mitochondrial DNA endonuclease involved in intron homing. It introduces a specific double-strand break in the DNA of the 21S rRNA gene and thus mediates the insertion of an intron, containing its own coding sequence (group I intron), into an intronless gene. Specifically recognizes and cleaves the sequence 5'-TAGGGATAACAGGGTAAT-3'.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

I-SceI is a homing endonuclease that specifically cleaves an 18-bp double-stranded DNA. I-SceI exhibits a strong preference for cleaving the bottom strand DNA. The published structure of I-SceI bound to an uncleaved DNA substrate provided a mechanism for bottom strand cleavage but not for top strand cleavage. To more fully elucidate the I-SceI catalytic mechanism, we determined the X-ray structures of I-SceI in complex with DNA substrates that are nicked in either the top or bottom strands. The structures resemble intermediates along the DNA cleavage reaction. In a structure containing a nick in the top strand, the spatial arrangement of metal ions is similar to that observed in the structure that contains uncleaved DNA, suggesting that cleavage of the bottom strand occurs by a common mechanism regardless of whether this strand is cleaved first or second. In the structure containing a nick in the bottom strand, a new metal binding site is present in the active site that cleaves the top strand. This new metal and a candidate nucleophilic water molecule are correctly positioned to cleave the top strand following bottom strand cleavage, providing a plausible mechanism for top strand cleavage.

Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.,Moure CM, Gimble FS, Quiocho FA Nucleic Acids Res. 2008 Jun;36(10):3287-96. Epub 2008 Apr 19. PMID:18424798^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Moure CM, Gimble FS, Quiocho FA. Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway. Nucleic Acids Res. 2008 Jun;36(10):3287-96. Epub 2008 Apr 19. PMID:18424798 doi:10.1093/nar/gkn178