4OQ2

5hmC specific restriction endonuclease PvuRTs1I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the 5hmC specific endonuclease PvuRts1I.

Kazrani, A.A.Kowalska, M.Czapinska, H.Bochtler, M.

(2014) Nucleic Acids Res. 42: 5929-5936

  • DOI: 10.1093/nar/gku186

  • PubMed Abstract: 
  • PvuRts1I is a prototype for a larger family of restriction endonucleases that cleave DNA containing 5-hydroxymethylcytosine (5hmC) or 5-glucosylhydroxymethylcytosine (5ghmC), but not 5-methylcytosine (5mC) or cytosine. Here, we report a crystal struc ...

    PvuRts1I is a prototype for a larger family of restriction endonucleases that cleave DNA containing 5-hydroxymethylcytosine (5hmC) or 5-glucosylhydroxymethylcytosine (5ghmC), but not 5-methylcytosine (5mC) or cytosine. Here, we report a crystal structure of the enzyme at 2.35 Å resolution. Although the protein has been crystallized in the absence of DNA, the structure is very informative. It shows that PvuRts1I consists of an N-terminal, atypical PD-(D/E)XK catalytic domain and a C-terminal SRA domain that might accommodate a flipped 5hmC or 5ghmC base. Changes to predicted catalytic residues of the PD-(D/E)XK domain or to the putative pocket for a flipped base abolish catalytic activity. Surprisingly, fluorescence changes indicative of base flipping are not observed when PvuRts1I is added to DNA substrates containing pyrrolocytosine in place of 5hmC (5ghmC). Despite this caveat, the structure suggests a model for PvuRts1I activity and presents opportunities for protein engineering to alter the enzyme properties for biotechnological applications.


    Organizational Affiliation

    International Institute of Molecular and Cell Biology, Trojdena 4, 02109 Warsaw, Poland mbochtler@iimcb.gov.pl.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Restriction endonuclease PvuRts1 I
A
303Proteus vulgarisMutation(s): 0 
Gene Names: pvuRts1I
Find proteins for Q52612 (Proteus vulgaris)
Go to UniProtKB:  Q52612
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 61.990α = 90.00
b = 61.990β = 90.00
c = 210.990γ = 90.00
Software Package:
Software NamePurpose
SHELXDEphasing
PHENIXphasing
PHENIXmodel building
XSCALEdata scaling
XDSdata reduction
DMphasing
DMmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-04-02
    Type: Database references
  • Version 1.2: 2014-06-04
    Type: Database references
  • Version 1.3: 2018-03-07
    Type: Data collection