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Structure Determination and Biochemical Characterization of a Putative HNH Endonuclease from Geobacter metallireducens GS-15
The crystal structure of a putative HNH endonuclease, Gmet_0936 protein from Geobacter metallireducens GS-15, has been determined at 2.6 Å resolution using single-wavelength anomalous dispersion method. The structure contains a two-stranded anti-parallel β-sheet that are surrounded by two helices on...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765158/ https://www.ncbi.nlm.nih.gov/pubmed/24039739 http://dx.doi.org/10.1371/journal.pone.0072114 |
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author | Xu, Shuang-yong Kuzin, Alexandre P. Seetharaman, Jayaraman Gutjahr, Alice Chan, Siu-Hong Chen, Yang Xiao, Rong Acton, Thomas B. Montelione, Gaetano T. Tong, Liang |
author_facet | Xu, Shuang-yong Kuzin, Alexandre P. Seetharaman, Jayaraman Gutjahr, Alice Chan, Siu-Hong Chen, Yang Xiao, Rong Acton, Thomas B. Montelione, Gaetano T. Tong, Liang |
author_sort | Xu, Shuang-yong |
collection | PubMed |
description | The crystal structure of a putative HNH endonuclease, Gmet_0936 protein from Geobacter metallireducens GS-15, has been determined at 2.6 Å resolution using single-wavelength anomalous dispersion method. The structure contains a two-stranded anti-parallel β-sheet that are surrounded by two helices on each face, and reveals a Zn ion bound in each monomer, coordinated by residues Cys38, Cys41, Cys73, and Cys76, which likely plays an important structural role in stabilizing the overall conformation. Structural homologs of Gmet_0936 include Hpy99I endonuclease, phage T4 endonuclease VII, and other HNH endonucleases, with these enzymes sharing 15–20% amino acid sequence identity. An overlay of Gmet_0936 and Hpy99I structures shows that most of the secondary structure elements, catalytic residues as well as the zinc binding site (zinc ribbon) are conserved. However, Gmet_0936 lacks the N-terminal domain of Hpy99I, which mediates DNA binding as well as dimerization. Purified Gmet_0936 forms dimers in solution and a dimer of the protein is observed in the crystal, but with a different mode of dimerization as compared to Hpy99I. Gmet_0936 and its N77H variant show a weak DNA binding activity in a DNA mobility shift assay and a weak Mn(2+)-dependent nicking activity on supercoiled plasmids in low pH buffers. The preferred substrate appears to be acid and heat-treated DNA with AP sites, suggesting Gmet_0936 may be a DNA repair enzyme. |
format | Online Article Text |
id | pubmed-3765158 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-37651582013-09-13 Structure Determination and Biochemical Characterization of a Putative HNH Endonuclease from Geobacter metallireducens GS-15 Xu, Shuang-yong Kuzin, Alexandre P. Seetharaman, Jayaraman Gutjahr, Alice Chan, Siu-Hong Chen, Yang Xiao, Rong Acton, Thomas B. Montelione, Gaetano T. Tong, Liang PLoS One Research Article The crystal structure of a putative HNH endonuclease, Gmet_0936 protein from Geobacter metallireducens GS-15, has been determined at 2.6 Å resolution using single-wavelength anomalous dispersion method. The structure contains a two-stranded anti-parallel β-sheet that are surrounded by two helices on each face, and reveals a Zn ion bound in each monomer, coordinated by residues Cys38, Cys41, Cys73, and Cys76, which likely plays an important structural role in stabilizing the overall conformation. Structural homologs of Gmet_0936 include Hpy99I endonuclease, phage T4 endonuclease VII, and other HNH endonucleases, with these enzymes sharing 15–20% amino acid sequence identity. An overlay of Gmet_0936 and Hpy99I structures shows that most of the secondary structure elements, catalytic residues as well as the zinc binding site (zinc ribbon) are conserved. However, Gmet_0936 lacks the N-terminal domain of Hpy99I, which mediates DNA binding as well as dimerization. Purified Gmet_0936 forms dimers in solution and a dimer of the protein is observed in the crystal, but with a different mode of dimerization as compared to Hpy99I. Gmet_0936 and its N77H variant show a weak DNA binding activity in a DNA mobility shift assay and a weak Mn(2+)-dependent nicking activity on supercoiled plasmids in low pH buffers. The preferred substrate appears to be acid and heat-treated DNA with AP sites, suggesting Gmet_0936 may be a DNA repair enzyme. Public Library of Science 2013-09-06 /pmc/articles/PMC3765158/ /pubmed/24039739 http://dx.doi.org/10.1371/journal.pone.0072114 Text en © 2013 Xu et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Xu, Shuang-yong Kuzin, Alexandre P. Seetharaman, Jayaraman Gutjahr, Alice Chan, Siu-Hong Chen, Yang Xiao, Rong Acton, Thomas B. Montelione, Gaetano T. Tong, Liang Structure Determination and Biochemical Characterization of a Putative HNH Endonuclease from Geobacter metallireducens GS-15 |
title | Structure Determination and Biochemical Characterization of a Putative HNH Endonuclease from Geobacter metallireducens GS-15 |
title_full | Structure Determination and Biochemical Characterization of a Putative HNH Endonuclease from Geobacter metallireducens GS-15 |
title_fullStr | Structure Determination and Biochemical Characterization of a Putative HNH Endonuclease from Geobacter metallireducens GS-15 |
title_full_unstemmed | Structure Determination and Biochemical Characterization of a Putative HNH Endonuclease from Geobacter metallireducens GS-15 |
title_short | Structure Determination and Biochemical Characterization of a Putative HNH Endonuclease from Geobacter metallireducens GS-15 |
title_sort | structure determination and biochemical characterization of a putative hnh endonuclease from geobacter metallireducens gs-15 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765158/ https://www.ncbi.nlm.nih.gov/pubmed/24039739 http://dx.doi.org/10.1371/journal.pone.0072114 |
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