Table 1.

Summary of crystallographic structures of the different homing endonuclease families

Family representative member	Oligomeric state	DNA bound? no. of bp	DNA curvature	DNA binding mode	Active site ions (no.)	No. of bp overhang after cleavage	Fold/catalytic residues	PDB code
LAGLIDADG (I-CreI & I-DmoI)	Dimer (I-CreI)	Yes 24-mer	45°	Endothermic [160]	3 Ca2+/3 Mg2+/3 Mn2+	4 bp	LAGLIDADG fold/acidic residues coordinate metal ion, metal dependent hydrolysis following an in-line displacement mechanism	1AF5 (apo) [161], 1BP7 (DNA bound) [21], 1g9z (Mg2+) & 1g9y (Ca2+) [31]
	Monomer (I-DmoI)	Yes 25-mer	40°	–	1 Ca2+/2 Mn2+	4 bp		1B24 (Apo [162]), 2VS7 (Ca2+), 2VS8 (Mn2+) [22]
HNH (I-HmuI)	Monomer	Yes 36-mer	40° 4–5 bp downstream to the cleavage site	Endothermic [160]	1 Mn2+	Nick	HNH fold/D74, N96, N99, H75/H75 is general base, ion is charge stabilizer	1U3E (Mn2+) [55]
His-Cys Box (I-PpoI)	Dimer	Yes 21-mer	55° across the central 4 bp	Exothermic [160]	Mg2+, Mn2+, Na+/1 ion per active site	4 (5 [65, 66])	HNH fold/D119, H98, C105, R61/H98 is general base, ion is charge stabilizer	1A73 (Mg2+), 1A74 (no ion) [68], 1CZ0 (Na+), 1CYQ (H98A), [70] 1EVX (apo), 1EVW(L116A) [71], 2O6 M (H98Q) [72]
GIY-YIG (I-TevI)	Catalytic domain Monomer	No	−40° toward the major groove after bottom strand cleavage [87]	NA	Mn2+/one ion per active site	2	Novel fold/E75, R27, Y17	1LN0, 1MKO (E75A mutant) [80]
	DNA-binding domain Monomer	Yes 21-mer	Mainly undistorted	NA	–	–	Zn finger- NUMOD3-IENR1 domains define cleavage site/	1I3 J [91], 1T2T [163]
PD-(D/E)XK (I-SspI)	Tetramer (only two active subunits)	Yes 29-mer	25° around the central bases	Exothermic [160]	Ca2+, Mg2+/one ion (Ca2+) per active site in mutant structure, wild type might have two ions per active site	3	PD-(D/E)-XK nuclease fold/acidic residues coordinate metal ion, metal dependent hydrolysis following an in-line displacement mechanism	2OST (Ca2+) [97]