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CSA entry for 1lws
Original Entry
Title:
Hydrolase/dna
Compound:
Endonuclease pi-scei
Mutant:
No
UniProt/Swiss-Prot:
P17255-VATA_YEAST
EC Class:
3.6.3.14
Other CSA Entries:
Overview of all sites for 1lws
Homologues of 1lws
Entries for UniProt/Swiss-Prot: P17255
Entries for EC: 3.6.3.14
Other Databases:
PDB entry: 1lws
PDBsum entry: 1lws
UniProt/Swiss-Prot: P17255
IntEnz entry: 3.6.3.14
Literature Report:
Introduction:
The homing endonuclease from S. cerevisiae, PI-SceI is able to catalyse the specific cleavage of double stranded DNA in order to allow the incorporation of a mobile intron into the allele. This enables non-mendelian propagation of certain introns without harming the target allele, as the introns are spliced out before functional mRNA is produced. It belongs to a large family of endonucleases all with the sequence LADLIDADG, and contains two active sites to allow simultaneous cleavage of both strands of DNA. The homing endonucleases in general are highly specific, and PI-SceI thus recognises a 31 base pair DNA sequence as its substrate, the longest specific sequence for a DNA binding protein yet discovered. This entry covers the active site which cleaves the top strand, running 5' to 3'.
Mechanism:
The cleavage of double stranded DNA occurs by nucleophilic attack from a water molecule activated by a Mg2+ ion at the active site on the phosphate to give a pentavalent phosphate transition state, stabilised by contact to the Mg2+ ion. Protonation of the 3' deoxyribose sugar by Lys 403 allows the cleavage of the backbone to release the two fragments.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 403 686Sidechain
Acid/baseSubstrate
Protonates the leaving group, facilitating collapse of the pentavalent phosphate transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10601013 Current protein Mutagenesis of residue
PubMed ID 10601013 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
CAA 502 0
ElectrostaticWater
ElectrostaticTransition state
Activates water to allow it to act as a nucleophile and attack the phosphodiester bond. Is also involved in stabilisation of the resultant pentavalent phosphate transition state which collapses to release the product.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11123916 Current protein Ligand is essential for catalysis
PubMed ID 12219083 Current protein Residue is positioned appropriately (ligand position known)
References:
1
Identification of Asp218 and Asp326 as the principal Mg2+ binding ligands of the homing endonuclease PI-SceI.
S. Schöttler and W. Wende and V. Pingoud and A. Pingoud
Biochemistry 39, (51) 15895-900, (2000).
11123916
2
Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.
C. M. Moure and F. S. Gimble and F. A. Quiocho
Nat Struct Biol 9, (10) 764-70, (2002).
12219083
3
The monomeric homing endonuclease PI-SceI has two catalytic centres for cleavage of the two strands of its DNA substrate.
F. Christ and S. Schoettler and W. Wende and S. Steuer and A. Pingoud and V. Pingoud
EMBO J 18, (24) 6908-16, (1999).
10601013
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