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

Abstract

AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves 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 themore » 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.« less

Authors:
; ; ; ; ; ; ; ; ;  [1];  [2]
  1. (Emory-MED)
  2. (
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH); USDOE Office of Science (SC)
OSTI Identifier:
1140052
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nucleic Acids Research; Journal Volume: 42; Journal Issue: 12
Country of Publication:
United States
Language:
ENGLISH
Subject:
63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTANT EFFECTS ON LIVING ORGS. AND BIOL. MAT.

Citation Formats

Horton, John R., Borgaro, Janine G., Griggs, Rose M., Quimby, Aine, Guan, Shengxi, Zhang, Xing, Wilson, Geoffrey G., Zheng, Yu, Zhu, Zhenyu, Cheng, Xiaodong, and NE Biolabs). Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA. United States: N. p., 2014. Web. doi:10.1093/nar/gku497.
Horton, John R., Borgaro, Janine G., Griggs, Rose M., Quimby, Aine, Guan, Shengxi, Zhang, Xing, Wilson, Geoffrey G., Zheng, Yu, Zhu, Zhenyu, Cheng, Xiaodong, & NE Biolabs). Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA. United States. doi:10.1093/nar/gku497.
Horton, John R., Borgaro, Janine G., Griggs, Rose M., Quimby, Aine, Guan, Shengxi, Zhang, Xing, Wilson, Geoffrey G., Zheng, Yu, Zhu, Zhenyu, Cheng, Xiaodong, and NE Biolabs). Thu . "Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA". United States. doi:10.1093/nar/gku497.
@article{osti_1140052,
title = {Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA},
author = {Horton, John R. and Borgaro, Janine G. and Griggs, Rose M. and Quimby, Aine and Guan, Shengxi and Zhang, Xing and Wilson, Geoffrey G. and Zheng, Yu and Zhu, Zhenyu and Cheng, Xiaodong and NE Biolabs)},
abstractNote = {AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves 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.},
doi = {10.1093/nar/gku497},
journal = {Nucleic Acids Research},
number = 12,
volume = 42,
place = {United States},
year = {Thu Jul 03 00:00:00 EDT 2014},
month = {Thu Jul 03 00:00:00 EDT 2014}
}