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 

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:  

  • 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 e ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Restriction endonuclease Hpy99I
A, B
200Helicobacter pylori (strain J99 / ATCC 700824)Mutation(s): 0 
Find proteins for Q9ZL26 (Helicobacter pylori (strain J99 / ATCC 700824))
Go to UniProtKB:  Q9ZL26
Entity ID: 2
MoleculeChainsLengthOrganism
5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3'C11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3'D11N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 90.089α = 90.00
b = 90.089β = 90.00
c = 334.254γ = 120.00
Software Package:
Software NamePurpose
MxCuBEdata collection
SHELXCDphasing
SHELXEmodel building
ARP/wARPmodel building
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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