3MQ6

Domain swapped SgrAI with DNA and calcium bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Domain swapping in allosteric modulation of DNA specificity.

Park, C.K.Joshi, H.K.Agrawal, A.Ghare, M.I.Little, E.J.Dunten, P.W.Bitinaite, J.Horton, N.C.

(2010) PLoS Biol 8: e1000554-e1000554

  • DOI: 10.1371/journal.pbio.1000554
  • Primary Citation of Related Structures:  
    3MQ6

  • PubMed Abstract: 
  • SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-modulation of cleavage activity and sequence specificity. Previous studies have shown that DNA bound dimers of SgrAI oligomerize into an activated form with higher DNA cleavage rates, although previously determined crystal structures of SgrAI bound to DNA show only the DNA bound dimer ...

    SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-modulation of cleavage activity and sequence specificity. Previous studies have shown that DNA bound dimers of SgrAI oligomerize into an activated form with higher DNA cleavage rates, although previously determined crystal structures of SgrAI bound to DNA show only the DNA bound dimer. A new crystal structure of the type II restriction endonuclease SgrAI bound to DNA and Ca(2+) is now presented, which shows the close association of two DNA bound SgrAI dimers. This tetrameric form is unlike those of the homologous enzymes Cfr10I and NgoMIV and is formed by the swapping of the amino-terminal 24 amino acid residues. Two mutations predicted to destabilize the swapped form of SgrAI, P27W and P27G, have been made and shown to eliminate both the oligomerization of the DNA bound SgrAI dimers as well as the allosteric stimulation of DNA cleavage by SgrAI. A mechanism involving domain swapping is proposed to explain the unusual allosteric properties of SgrAI via association of the domain swapped tetramer of SgrAI bound to DNA into higher order oligomers.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SgraIR restriction enzymeA, B, C, D, E, F, G, H338Streptomyces griseusMutation(s): 0 
Gene Names: sgraIR
EC: 3.1.21.4
UniProt
Find proteins for Q9F6L0 (Streptomyces griseus)
Explore Q9F6L0 
Go to UniProtKB:  Q9F6L0
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')J [auth K], I [auth L], L [auth M], K [auth N], N [auth O], M [auth P], P [auth Q], O [auth R]17N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CA
    Query on CA

    Download Ideal Coordinates CCD File 
    AA [auth D] , BA [auth D] , CA [auth E] , DA [auth E] , EA [auth F] , FA [auth F] , GA [auth F] , HA [auth G] , 
    AA [auth D], BA [auth D], CA [auth E], DA [auth E], EA [auth F], FA [auth F], GA [auth F], HA [auth G], IA [auth G], JA [auth H], KA [auth H], LA [auth H], Q [auth A], R [auth A], S [auth A], T [auth B], U [auth B], V [auth B], W [auth C], X [auth C], Y [auth C], Z [auth D]
    CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.261 
    • R-Value Work: 0.211 
    • R-Value Observed: 0.212 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 130.384α = 90
    b = 134.949β = 90
    c = 237.485γ = 90
    Software Package:
    Software NamePurpose
    Blu-Icedata collection
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2010-11-10
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance