2DCH

Crystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I

Summary for 2DCH

• Entry DOI: 10.2210/pdb2dch/pdb
• Descriptor: putative homing endonuclease, CHLORIDE ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: alpha/beta fold, hydrolase
• Biological source: Thermoproteus
• Total number of polymer chains: 1
• Total formula weight: 24889.89

Authors

Nakayama, H.,Tsuge, H.,Shimamura, T.,Miyano, M.,Nomura, N.,Sako, Y. (deposition date: 2006-01-06, release date: 2006-07-06, Last modification date: 2024-03-13)

Primary citation

Nakayama, H.,Shimamura, T.,Imagawa, T.,Shirai, N.,Itoh, T.,Sako, Y.,Miyano, M.,Sakuraba, H.,Ohshima, T.,Nomura, N.,Tsuge, H.
Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: contribution of cross-domain polar networks to thermostability.
J.Mol.Biol., 365:362-378, 2007

PubMed Abstract: A novel LAGLIDADG-type homing endonuclease (HEase), I-Tsp061I, from the hyperthermophilic archaeon Thermoproteus sp. IC-061 16 S rRNA gene (rDNA) intron was characterized with respect to its structure, catalytic properties and thermostability. It was found that I-Tsp061I is a HEase isoschizomer of the previously described I-PogI and exhibits the highest thermostability among the known LAGLIDADG-type HEases. Determination of the crystal structure of I-Tsp061I at 2.1 A resolution using the multiple isomorphous replacement and anomalous scattering method revealed that the overall fold is similar to that of other known LAGLIDADG-type HEases, despite little sequence similarity between I-Tsp061I and those HEases. However, I-Tsp061I contains important cross-domain polar networks, unlike its mesophilic counterparts. Notably, the polar network Tyr6-Asp104-His180-107O-HOH12-104O-Asn177 exists across the two packed alpha-helices containing both the LAGLIDADG catalytic motif and the GxxxG hydrophobic helix bundle motif. Another important structural feature is the salt-bridge network Asp29-Arg31-Glu182 across N and C-terminal domain interface, which appears to contribute to the stability of the domain/domain packing. On the basis of these structural analyses and extensive mutational studies, we conclude that such cross-domain polar networks play key roles in stabilizing the catalytic center and domain packing, and underlie the hyperthermostability of I-Tsp061I.

PubMed: 17069851
DOI: 10.1016/j.jmb.2006.09.066

Experimental method

X-RAY DIFFRACTION (2.06 Å)