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Title: Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å

Abstract

HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG↓C-3' in duplex DNA and cleaves (‘↓’) to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 Å. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded β sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the ‘PD-D/EXK’ superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G↓CGC) and MspI (C↓CGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biologicalmore » methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.« less

Authors:
 [1];  [1];  [1];  [2];  [2];  [2];  [2]; ORCiD logo [1]
  1. Univ. of Texas, Houston, TX (United States). Anderson Cancer Center
  2. New England Biolabs, Inc., Ipswich, MA (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH)
OSTI Identifier:
1603149
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 48; Journal Issue: 3; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Horton, John R., Yang, Jie, Zhang, Xing, Petronzio, Theresa, Fomenkov, Alexey, Wilson, Geoffrey G., Roberts, Richard J., and Cheng, Xiaodong. Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å. United States: N. p., 2019. Web. https://doi.org/10.1093/nar/gkz1195.
Horton, John R., Yang, Jie, Zhang, Xing, Petronzio, Theresa, Fomenkov, Alexey, Wilson, Geoffrey G., Roberts, Richard J., & Cheng, Xiaodong. Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å. United States. https://doi.org/10.1093/nar/gkz1195
Horton, John R., Yang, Jie, Zhang, Xing, Petronzio, Theresa, Fomenkov, Alexey, Wilson, Geoffrey G., Roberts, Richard J., and Cheng, Xiaodong. Fri . "Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å". United States. https://doi.org/10.1093/nar/gkz1195. https://www.osti.gov/servlets/purl/1603149.
@article{osti_1603149,
title = {Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å},
author = {Horton, John R. and Yang, Jie and Zhang, Xing and Petronzio, Theresa and Fomenkov, Alexey and Wilson, Geoffrey G. and Roberts, Richard J. and Cheng, Xiaodong},
abstractNote = {HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG↓C-3' in duplex DNA and cleaves (‘↓’) to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 Å. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded β sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the ‘PD-D/EXK’ superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G↓CGC) and MspI (C↓CGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.},
doi = {10.1093/nar/gkz1195},
journal = {Nucleic Acids Research},
number = 3,
volume = 48,
place = {United States},
year = {2019},
month = {12}
}

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