PDBsum entry 3c0x

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protein dna_rna metals links
Hydrolase/DNA PDB id
Protein chain
223 a.a. *
_CA ×3
Waters ×58
* Residue conservation analysis
PDB id:
Name: Hydrolase/DNA
Title: I-scei in complex with a top nicked DNA substrate
Structure: Intron-encoded endonuclease i-scei. Chain: a. Synonym: 21s rrna intron maturase, homing endonuclease omega. Engineered: yes. DNA (5'- d( Dc Dap Dcp Dgp Dcp Dtp Dap Dgp Dgp Dgp Dap Dtp Dap Da)- 3'). Chain: b.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: scei, omega, secy. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: DNA synthetic product. Other_details: DNA synthetic product
2.30Å     R-factor:   0.255     R-free:   0.288
Authors: C.M.Moure,F.S.Gimble,F.A.Quiocho
Key ref: C.M.Moure et al. (2008). 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. PubMed id: 18424798
21-Jan-08     Release date:   06-May-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P03882  (SCE1_YEAST) -  Intron-encoded endonuclease I-SceI
235 a.a.
223 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   1 term 
  Biological process     nucleic acid phosphodiester bond hydrolysis   4 terms 
  Biochemical function     hydrolase activity     3 terms  


Nucleic Acids Res 36:3287-3296 (2008)
PubMed id: 18424798  
Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.
C.M.Moure, F.S.Gimble, F.A.Quiocho.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21220111 B.L.Stoddard (2011).
Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification.
  Structure, 19, 7.  
20805246 S.H.Chan, B.L.Stoddard, and S.Y.Xu (2011).
Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity.
  Nucleic Acids Res, 39, 1.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
19811621 H.Gao, J.Smith, M.Yang, S.Jones, V.Djukanovic, M.G.Nicholson, A.West, D.Bidney, S.C.Falco, D.Jantz, and L.A.Lyznik (2010).
Heritable targeted mutagenesis in maize using a designed endonuclease.
  Plant J, 61, 176-187.  
19915993 M.J.Marcaida, I.G.Muñoz, F.J.Blanco, J.Prieto, and G.Montoya (2010).
Homing endonucleases: from basics to therapeutic applications.
  Cell Mol Life Sci, 67, 727-748.  
19276110 A.McConnell Smith, R.Takeuchi, S.Pellenz, L.Davis, N.Maizels, R.J.Monnat, and B.L.Stoddard (2009).
Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease.
  Proc Natl Acad Sci U S A, 106, 5099-5104.  
18974222 M.J.Marcaida, J.Prieto, P.Redondo, A.D.Nadra, A.Alibés, L.Serrano, S.Grizot, P.Duchateau, F.Pâques, F.J.Blanco, and G.Montoya (2008).
Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering.
  Proc Natl Acad Sci U S A, 105, 16888-16893.
PDB codes: 2vs7 2vs8
18644379 Y.Niu, K.Tenney, H.Li, and F.S.Gimble (2008).
Engineering variants of the I-SceI homing endonuclease with strand-specific and site-specific DNA-nicking activity.
  J Mol Biol, 382, 188-202.  
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