PDBsum entry 2dch

Hydrolase

PDB id: 2dch

Contents

Protein chain

204 a.a. *

Ligands

SO4 ×2

Metals

_CL

Waters ×172

* Residue conservation analysis

PDB id:

2dch

Name:

Hydrolase

Title:

Crystal structure of archaeal intron-encoded homing endonuclease i- tsp061i

Structure:

Putative homing endonuclease. Chain: x. Synonym: archaeal intron-encoded DNA endonuclease. Engineered: yes

Source:

Thermoproteus. Organism_taxid: 2270. Strain: ic-061. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.06Å R-factor: 0.204 R-free: 0.243

Authors:

H.Nakayama,H.Tsuge,T.Shimamura,M.Miyano,N.Nomura,Y.Sako

Key ref:

H.Nakayama et al. (2007). Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: contribution of cross-domain polar networks to thermostability. J Mol Biol, 365, 362-378. PubMed id: 17069851

Date:

06-Jan-06 Release date: 06-Jul-06

Protein chain

Q8J309  (Q8J309_9CREN) -  Putative homing endonuclease from Thermoproteus sp. IC-062

Seq: 203 a.a.

Struc: 204 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.-.-

J Mol Biol 365:362-378 (2007)

PubMed id: 17069851

Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: contribution of cross-domain polar networks to thermostability.

H.Nakayama, T.Shimamura, T.Imagawa, N.Shirai, T.Itoh, Y.Sako, M.Miyano, H.Sakuraba, T.Ohshima, N.Nomura, H.Tsuge.

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.