A spindle-shaped virus protein (chymotrypsin treated)

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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

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

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

  • DOI: https://doi.org/10.1107/S0907444912007202
  • Primary Citation of Related Structures:  
    3VCF, 4DKS

  • 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.

  • Organizational Affiliation

    State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable integrase162Sulfolobus spindle-shaped virus 1Mutation(s): 0 
Gene Names: d335
Find proteins for P20214 (Sulfolobus spindle-shape virus 1)
Explore P20214 
Go to UniProtKB:  P20214
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20214
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.224α = 90
b = 75.224β = 90
c = 96.091γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references, Derived calculations