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PDBsum entry 3c0x

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protein dna_rna metals links
Hydrolase/DNA PDB id
3c0x
Jmol
Contents
Protein chain
223 a.a. *
DNA/RNA
Metals
_CA ×3
Waters ×58
* Residue conservation analysis
PDB id:
3c0x
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
Resolution:
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
Date:
21-Jan-08     Release date:   06-May-08    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03882  (SCE1_YEAST) -  Intron-encoded endonuclease I-SceI
Seq:
Struc:
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.
 
  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.
 

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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.