1CYQ image
Deposition Date 1999-08-31
Release Date 1999-11-19
Last Version Date 2024-02-07
Entry Detail
PDB ID:
1CYQ
Keywords:
HYDROLASE/DNA
Title:
INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX
Biological Source:
Source Organism:
Physarum polycephalum (Taxon ID: 5791)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.93 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 31 2 1
1CYQ validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:INTRON-ENCODED HOMING ENDONUCLEASE I-PPOI
Mutagens:H98A
Chain IDs:C (auth: A), D (auth: B)
Chain Length:162
Number of Molecules:2
Biological Source:Physarum polycephalum
UniProt ID:Q94702 Pfam ID:PF05551
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3'
Chain IDs:A (auth: C), B (auth: D)
Chain Length:21
Number of Molecules:2
Biological Source:
Ligand Molecules
MG
ZN
Primary Citation
A novel endonuclease mechanism directly visualized for I-PpoI.
Nat.Struct.Biol. 6 1096 1099 (1999)
PMID: 10581547 DOI: 10.1038/70027

Abstact

A novel mechanism of DNA endonucleolytic cleavage has been visualized for the homing endonuclease I-PpoI by trapping the uncleaved enzyme-substrate complex and comparing it to the previously visualized product complex. This enzyme employs a unique single metal mechanism. A magnesium ion is coordinated by an asparagine residue and two DNA oxygen atoms and stabilizes the phosphoanion transition state and the 3'oxygen leaving group. A hydrolytic water molecule is activated by a histidine residue for an in-line attack on the scissile phosphate. A strained enzyme-substrate-metal complex is formed before cleavage, then relaxed during the reaction.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
1A73
1A74
1IPP
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