1YF2

Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications.

Kim, J.S., Degiovanni, A., Jancarik, J., Adams, P.D., Yokota, H., Kim, R., Kim, S.H.

(2005) Proc Natl Acad Sci U S A 102: 3248-3253

  • DOI: 10.1073/pnas.0409851102
  • Primary Citation of Related Structures:  
    1YF2

  • PubMed Abstract: 

    • Type I restriction-modification enzymes are differentiated from type II and type III enzymes by their recognition of two specific dsDNA sequences separated by a given spacer and cleaving DNA randomly away from the recognition sites. They are oligomeric proteins formed by three subunits: a specificity subunit, a methylation subunit, and a restriction subunit ...

    Type I restriction-modification enzymes are differentiated from type II and type III enzymes by their recognition of two specific dsDNA sequences separated by a given spacer and cleaving DNA randomly away from the recognition sites. They are oligomeric proteins formed by three subunits: a specificity subunit, a methylation subunit, and a restriction subunit. We solved the crystal structure of a specificity subunit from Methanococcus jannaschii at 2.4-A resolution. Two highly conserved regions (CRs) in the middle and at the C terminus form a coiled-coil of long antiparallel alpha-helices. Two target recognition domains form globular structures with almost identical topologies and two separate DNA binding clefts with a modeled DNA helix axis positioned across the CR helices. The structure suggests that the coiled-coil CRs act as a molecular ruler for the separation between two recognized DNA sequences. Furthermore, the relative orientation of the two DNA binding clefts suggests kinking of bound dsDNA and exposing of target adenines from the recognized DNA sequences.

    Organizational Affiliation: 

    Department of Chemistry, University of California, Berkeley, CA 94720, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Type I restriction-modification enzyme, S subunitA, B425Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: MJ0130
UniProt
Find proteins for Q57594 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57594 
Go to UniProtKB:  Q57594
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57594
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.972α = 90
b = 94.222β = 95.01
c = 103.52γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance