3FC3

Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.

Sokolowska, M.Czapinska, H.Bochtler, M.

(2009) Nucleic Acids Res 37: 3799-3810

  • DOI: 10.1093/nar/gkp228
  • Primary Citation of Related Structures:  
    3GOX, 3FC3

  • PubMed Abstract: 
  • The beta beta alpha-Me restriction endonuclease (REase) Hpy99I recognizes the CGWCG target sequence and cleaves it with unusual stagger (five nucleotide 5'-recessed ends). Here we present the crystal structure of the specific complex of the dimeric enzyme with DNA ...

    The beta beta alpha-Me restriction endonuclease (REase) Hpy99I recognizes the CGWCG target sequence and cleaves it with unusual stagger (five nucleotide 5'-recessed ends). Here we present the crystal structure of the specific complex of the dimeric enzyme with DNA. The Hpy99I protomer consists of an antiparallel beta-barrel and two beta 4 alpha 2 repeats. Each repeat coordinates a structural zinc ion with four cysteine thiolates in two CXXC motifs. The beta beta alpha-Me region of the second beta 4 alpha 2 repeat holds the catalytic metal ion (or its sodium surrogate) via Asp148 and Asn165 and activates a water molecule with the general base His149. In the specific complex, Hpy99I forms a ring-like structure around the DNA that contacts DNA bases on the major and minor groove sides via the first and second beta 4 alpha 2 repeats, respectively. Hpy99I interacts with the central base pair of the recognition sequence only on the minor groove side, where A:T resembles T:A and G:C is similar to C:G. The Hpy99I-DNA co-crystal structure provides the first detailed illustration of the beta beta alpha-Me site in REases and complements structural information on the use of this active site motif in other groups of endonucleases such as homing endonucleases (e.g. I-PpoI) and Holliday junction resolvases (e.g. T4 endonuclease VII).


    Related Citations: 
    • Crystal structure of T4 endonuclease VII resolving a Holliday junction.
      Biertumpfel, C., Yang, W., Suck, D.
      (2007) Nature 449: 616
    • DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
      Flick, K.E., Jurica, M.S., Monnat, R.J., Stoddard, B.L.
      (1998) Nature 394: 96

    Organizational Affiliation

    International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Restriction endonuclease Hpy99IA, B200Helicobacter pylori J99Mutation(s): 0 
Gene Names: jhp_0755synthetic gene codon optimized for Escherichia coli
UniProt
Find proteins for Q9ZL26 (Helicobacter pylori (strain J99 / ATCC 700824))
Explore Q9ZL26 
Go to UniProtKB:  Q9ZL26
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3'C11N/A
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3'D11N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.75 Å
      • R-Value Free: 0.205 
      • R-Value Work: 0.181 
      • R-Value Observed: 0.182 
      • Space Group: H 3 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 90.089α = 90
      b = 90.089β = 90
      c = 334.254γ = 120
      Software Package:
      Software NamePurpose
      MxCuBEdata collection
      SHELXCDphasing
      SHELXDphasing
      SHELXEmodel building
      ARP/wARPmodel building
      REFMACrefinement
      XDSdata reduction
      XSCALEdata scaling

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2009-03-31
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Source and taxonomy, Version format compliance
      • Version 1.2: 2017-11-01
        Changes: Refinement description