3VCF

SSV1 integrase C-terminal catalytic domain (174-335aa)

Summary for 3VCF

• Entry DOI: 10.2210/pdb3vcf/pdb
• Related: 4DKS
• Descriptor: Probable integrase (2 entities in total)
• Functional Keywords: catalyzes site-specific integration, recombination
• Biological source: Sulfolobus virus 1
• Total number of polymer chains: 2
• Total formula weight: 38507.02

Authors

Ouyang, S.,Liang, W.,Huang, L.,Liu, Z.-J. (deposition date: 2012-01-04, release date: 2012-05-30, Last modification date: 2024-10-09)

Primary citation

Zhan, Z.,Ouyang, S.,Liang, W.,Zhang, Z.,Liu, Z.J.,Huang, L.
Structural and functional characterization of the C-terminal catalytic domain of SSV1 integrase.
Acta Crystallogr.,Sect.D, 68:659-670, 2012

PubMed 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.

PubMed: 22683788
DOI: 10.1107/S0907444912007202

Experimental method

X-RAY DIFFRACTION (2.7 Å)