The 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI in a Complex with Product-like DNA

Experimental Data Snapshot

  • Resolution: 2.89 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history


Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA.

Horton, J.R.Borgaro, J.G.Griggs, R.M.Quimby, A.Guan, S.Zhang, X.Wilson, G.G.Zheng, Y.Zhu, Z.Cheng, X.

(2014) Nucleic Acids Res. 42: 7947-7959

  • DOI: 10.1093/nar/gku497
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves deoxyribonucleic acid (DNA) containing 5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA containing unmodified cytosine. AbaSI ...

    AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves deoxyribonucleic acid (DNA) containing 5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA containing unmodified cytosine. AbaSI has been used as a tool for mapping the genomic locations of 5hmC, an important epigenetic modification in the DNA of higher organisms. Here we report the crystal structures of AbaSI in the presence and absence of DNA. These structures provide considerable, although incomplete, insight into how this enzyme acts. AbaSI appears to be mainly a homodimer in solution, but interacts with DNA in our structures as a homotetramer. Each AbaSI subunit comprises an N-terminal, Vsr-like, cleavage domain containing a single catalytic site, and a C-terminal, SRA-like, 5hmC-binding domain. Two N-terminal helices mediate most of the homodimer interface. Dimerization brings together the two catalytic sites required for double-strand cleavage, and separates the 5hmC binding-domains by ∼70 Å, consistent with the known activity of AbaSI which cleaves DNA optimally between symmetrically modified cytosines ∼22 bp apart. The eukaryotic SET and RING-associated (SRA) domains bind to DNA containing 5-methylcytosine (5mC) in the hemi-methylated CpG sequence. They make contacts in both the major and minor DNA grooves, and flip the modified cytosine out of the helix into a conserved binding pocket. In contrast, the SRA-like domain of AbaSI, which has no sequence specificity, contacts only the minor DNA groove, and in our current structures the 5hmC remains intra-helical. A conserved, binding pocket is nevertheless present in this domain, suitable for accommodating 5hmC and g5hmC. We consider it likely, therefore, that base-flipping is part of the recognition and cleavage mechanism of AbaSI, but that our structures represent an earlier, pre-flipped stage, prior to actual recognition.

    Related Citations: 
    • Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine.
      Wang, H.,Guan, S.,Quimby, A.,Cohen-Karni, D.,Pradhan, S.,Wilson, G.,Roberts, R.J.,Zhu, Z.,Zheng, Y.
      (2011) Nucleic Acids Res. 39: 9294
    • Characterization of the 5-hydroxymethylcytosine-specific DNA restriction endonucleases.
      Borgaro, J.G.,Zhu, Z.
      (2013) Nucleic Acids Res. 41: 4198
    • High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells.
      Sun, Z.,Terragni, J.,Jolyon, T.,Borgaro, J.G.,Liu, Y.,Yu, L.,Guan, S.,Wang, H.,Sun, D.,Cheng, X.,Zhu, Z.,Pradhan, S.,Zheng, Y.
      (2013) Cell Rep 3: 567

    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA.


Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein AbaSI
B, A, C, D
321Acinetobacter baumannii (strain SDF)Mutation(s): 3 
Find proteins for B0VN39 (Acinetobacter baumannii (strain SDF))
Go to UniProtKB:  B0VN39
Entity ID: 1
DNA 18-MERE,F18T4virus
Entity ID: 2
DNA 14-MERG,H14T4virus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on EDO

Download SDF File 
Download CCD File 
C2 H6 O2
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
Query on 5HC
E, F
Experimental Data & Validation

Experimental Data

  • Resolution: 2.89 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.826α = 90.00
b = 144.704β = 94.57
c = 105.033γ = 90.00
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM049245-20

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-08-06
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary