PDBsum entry 4dks

Recombination

PDB id: 4dks

Contents

Protein chain

145 a.a.

Waters ×67

PDB id:

4dks

Name:

Recombination

Title:

A spindle-shaped virus protein (chymotrypsin treated)

Structure:

Probable integrase. Chain: a. Engineered: yes

Source:

Sulfolobus virus 1. Organism_taxid: 244589. Gene: d335. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.70Å R-factor: 0.205 R-free: 0.261

Authors:

S.Ouyang,W.Liang,L.Huang,Z.-J.Liu

Key ref:

Z.Zhan et al. (2012). Structural and functional characterization of the C-terminal catalytic domain of SSV1 integrase. Acta Crystallogr D Biol Crystallogr, 68, 659-670. PubMed id: 22683788

Date:

04-Feb-12 Release date: 30-May-12

Protein chain

P20214  (VINT_SSV1) -  Integrase from Sulfolobus spindle-shape virus 1

Seq: 335 a.a.

Struc: 145 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.- - ?????
• Enzyme class 2: E.C.3.1.-.-

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Acta Crystallogr D Biol Crystallogr 68:659-670 (2012)

PubMed id: 22683788

Structural and functional characterization of the C-terminal catalytic domain of SSV1 integrase.

Z.Zhan, S.Ouyang, W.Liang, Z.Zhang, Z.J.Liu, L.Huang.

ABSTRACT

The spindle-shaped virus SSV1 of the hyperthermophilic archaeon Sulfolobus shibatae encodes an integrase (SSV1 Int). Here, the crystal structure of the C-terminal catalytic domain of SSV1 Int is reported. This is the first structural study of an archaeal tyrosine recombinase. Structural comparison shows that the C-terminal domain of SSV1 Int possesses a core fold similar to those of tyrosine recombinases of both bacterial and eukaryal origin, apart from the lack of a conserved helix corresponding to αI of Cre, indicating conservation of these enzymes among all three domains of life. Five of the six catalytic residues cluster around a basic cleft on the surface of the structure and the nucleophile Tyr314 is located on a flexible loop that stretches away from the central cleft, supporting the possibility that SSV1 Int cleaves the target DNA in a trans mode. Biochemical analysis suggests that the N-terminal domain is responsible for the dimerization of SSV1 Int. The C-terminal domain is capable of DNA cleavage and ligation, but at efficiencies significantly lower than those of the full-length protein. In addition, neither the N-terminal domain alone nor the C-terminal domain alone shows a strong sequence preference in DNA binding. Therefore, recognition of the core-type sequence and efficient catalysis by SSV1 Int presumably requires covalent linkage and interdomain communication between the two domains.