3C0X

I-SceI in complex with a top nicked DNA substrate

Summary for 3C0X

• Entry DOI: 10.2210/pdb3c0x/pdb
• Related: 1R7M 3COW
• Descriptor: DNA (5'-D(*DC*DAP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DAP*DA)-3'), DNA (5'-D(P*DCP*DAP*DGP*DGP*DGP*DTP*DAP*DAP*DTP*DAP*DC)-3'), DNA (5'-D(*DG*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DT)-3'), ... (6 entities in total)
• Functional Keywords: endonuclease, homing, ladlidadg, catalytic mechanism, metal binding, nicked intermediate, hydrolase, intron homing, mitochondrion, mrna processing, mrna splicing, hydrolase-dna complex, hydrolase/dna
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Cellular location: Mitochondrion: P03882
• Total number of polymer chains: 4
• Total formula weight: 43149.43

Authors

Moure, C.M.,Gimble, F.S.,Quiocho, F.A. (deposition date: 2008-01-21, release date: 2008-05-06, Last modification date: 2023-08-30)

Primary citation

Moure, C.M.,Gimble, F.S.,Quiocho, F.A.
Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.
Nucleic Acids Res., 36:3287-3296, 2008

PubMed Abstract: 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.

PubMed: 18424798
DOI: 10.1093/nar/gkn178

Experimental method

X-RAY DIFFRACTION (2.3 Å)