DNA Repair, volume 4, issue 3, pages 327-339
Solution-state NMR investigation of DNA binding interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): a dynamic description of the DNA/protein interface
2
Department of Computer Science and Electrical Engineering, Washington State University Tri-Cities, Richland, WA 99352, USA
|
3
Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA.
|
Publication type: Journal Article
Publication date: 2005-03-01
Biochemistry
Molecular Biology
Cell Biology
Abstract
Formamidopyrimidine-DNA glycosylase (Fpg) is a base excision repair (BER) protein that removes oxidative DNA lesions. Recent crystal structures of Fpg bound to DNA revealed residues involved in damage recognition and enzyme catalysis, but failed to shed light on the dynamic nature of the processes. To examine the structural and dynamic changes that occur in solution when Fpg binds DNA, NMR spectroscopy was used to study Escherichia coli Fpg free in solution and bound to a double-stranded DNA oligomer containing 1,3-propanediol (13-PD), a non-hydrolyzable abasic-site analogue. Only 209 out of a possible 251 (83%) free-precession 15N/1H HSQC cross peaks were observed and 180 of these were assignable, indicating that approximately 30% of the residues undergo intermediate motion on the NMR timescale, broadening the resonances beyond detection or making them intractable in backbone assignment experiments. The majority of these affected residues were in the polypeptide linker region and the interface between the N- and C-terminal domains. DNA titration experiments revealed line broadening and chemical shift perturbations for backbone amides nearby and distant from the DNA binding surface, but failed to quench the intermediate timescale motion observed for free Fpg, including those residues directly involved in DNA binding, notwithstanding a nanomolar dissociation constant for 13-PD binding. Indeed, after binding to 13-PD, at least approximately 40% of the Fpg residues undergo intermediate timescale motion even though all other residues exhibit tight DNA binding characteristic of slow exchange. CPMG-HSQC experiments revealed millisecond to microsecond motion for the backbone amides of D91 and H92 that were quenched upon binding 13-PD. In free Fpg, heteronuclear 1H-15N NOE experiments detected picosecond timescale backbone motion in the alphaF-beta9 loop, the region primarily responsible for chemically discriminating 8-oxoguanine (8-oxoG) over normal guanine, that was quenched after binding 13-PD. Collectively, these observations reveal that, in solution, Fpg is a very dynamic molecule even after binding damaged DNA. Such motion, especially at the DNA binding surface, may be key to its processive search for DNA damage and its catalytic functions once it recognizes damaged DNA.
Citations by journals
|
1
2
3
4
5
|
|
|
Biomolecular NMR Assignments
|
Biomolecular NMR Assignments
5 publications, 25%
|
|
Biochimica et Biophysica Acta - Proteins and Proteomics
|
Biochimica et Biophysica Acta - Proteins and Proteomics
2 publications, 10%
|
|
Chemistry & Biology
|
Chemistry & Biology
1 publication, 5%
|
|
Computational and Structural Biotechnology Journal
|
Computational and Structural Biotechnology Journal
1 publication, 5%
|
|
DNA Repair
|
DNA Repair
1 publication, 5%
|
|
Tuberculosis
|
Tuberculosis
1 publication, 5%
|
|
FEBS Letters
|
FEBS Letters
1 publication, 5%
|
|
Biochemistry
|
Biochemistry
1 publication, 5%
|
|
The Analyst
|
The Analyst
1 publication, 5%
|
|
Molecular BioSystems
|
Molecular BioSystems, 1, 5%
Molecular BioSystems
1 publication, 5%
|
|
Molecular Biology
|
Molecular Biology
1 publication, 5%
|
|
Nucleic Acids Research
|
Nucleic Acids Research
1 publication, 5%
|
|
Journal of Bacteriology
|
Journal of Bacteriology
1 publication, 5%
|
|
1
2
3
4
5
|
Citations by publishers
|
1
2
3
4
5
6
|
|
|
Elsevier
|
Elsevier
6 publications, 30%
|
|
Springer Nature
|
Springer Nature
5 publications, 25%
|
|
Wiley
|
Wiley
1 publication, 5%
|
|
American Chemical Society (ACS)
|
American Chemical Society (ACS)
1 publication, 5%
|
|
Royal Society of Chemistry (RSC)
|
Royal Society of Chemistry (RSC)
1 publication, 5%
|
|
|
, 1, 5%
1 publication, 5%
|
|
Pleiades Publishing
|
Pleiades Publishing
1 publication, 5%
|
|
Oxford University Press
|
Oxford University Press
1 publication, 5%
|
|
American Society for Microbiology
|
American Society for Microbiology
1 publication, 5%
|
|
1
2
3
4
5
6
|
- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
{"yearsCitations":{"type":"bar","data":{"show":true,"labels":[2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2021],"ids":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"codes":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"imageUrls":["","","","","","","","","","","","","","","","",""],"datasets":[{"label":"Citations number","data":[1,2,2,4,2,2,2,0,0,0,1,0,0,1,0,1,2],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":["5","10","10","20","10","10","10",0,0,0,"5",0,0,"5",0,"5","10"],"barThickness":null}]},"options":{"indexAxis":"x","maintainAspectRatio":true,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":1,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Citations per year","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"journals":{"type":"bar","data":{"show":true,"labels":["Biomolecular NMR Assignments","Biochimica et Biophysica Acta - Proteins and Proteomics","Chemistry & Biology","Computational and Structural Biotechnology Journal","DNA Repair","Tuberculosis","FEBS Letters","Biochemistry","The Analyst","Molecular BioSystems","Molecular Biology","Nucleic Acids Research","Journal of Bacteriology"],"ids":[15938,11289,25570,4268,13424,16282,405,9964,9343,25317,1134,23904,21892],"codes":[0,0,0,0,0,0,0,0,0,0,0,0,0],"imageUrls":["\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/leiAYcRDGTSl5B1eCnwpSGqmDEUEfDPPoYisFGhT_medium.webp","","\/storage\/images\/resized\/oZgeErrVFhuDksyqFURLvYS1wtVSBWczh001igGo_medium.webp","\/storage\/images\/resized\/yNSijlgQghQF53VZuyFLA30CKDe4j3HK74Vtpnxa_medium.webp","\/storage\/images\/resized\/VPE7q24PXoHr5SS2SqfEgxccSMUxWLfZINOX60uo_medium.webp"],"datasets":[{"label":"","data":[5,2,1,1,1,1,1,1,1,1,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[25,10,5,5,5,5,5,5,5,5,5,5,5],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Journals","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"publishers":{"type":"bar","data":{"show":true,"labels":["Elsevier","Springer Nature","Wiley","American Chemical Society (ACS)","Royal Society of Chemistry (RSC)","","Pleiades Publishing","Oxford University Press","American Society for Microbiology"],"ids":[17,8,11,40,123,6887,101,19,142],"codes":[0,0,0,0,0,0,0,0,0],"imageUrls":["\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/leiAYcRDGTSl5B1eCnwpSGqmDEUEfDPPoYisFGhT_medium.webp","","\/storage\/images\/resized\/oZgeErrVFhuDksyqFURLvYS1wtVSBWczh001igGo_medium.webp","\/storage\/images\/resized\/yNSijlgQghQF53VZuyFLA30CKDe4j3HK74Vtpnxa_medium.webp","\/storage\/images\/resized\/VPE7q24PXoHr5SS2SqfEgxccSMUxWLfZINOX60uo_medium.webp"],"datasets":[{"label":"","data":[6,5,1,1,1,1,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[30,25,5,5,5,5,5,5,5],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Publishers","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}}}
Metrics
Cite this
GOST |
RIS |
BibTex |
MLA
Cite this
GOST
Copy
Buchko G. W. et al. Solution-state NMR investigation of DNA binding interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): a dynamic description of the DNA/protein interface // DNA Repair. 2005. Vol. 4. No. 3. pp. 327-339.
GOST all authors (up to 50)
Copy
Buchko G. W., McAteer K., Wallace S. E., Kennedy M. Solution-state NMR investigation of DNA binding interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): a dynamic description of the DNA/protein interface // DNA Repair. 2005. Vol. 4. No. 3. pp. 327-339.
Cite this
RIS
Copy
TY - JOUR
DO - 10.1016/j.dnarep.2004.09.012
UR - https://doi.org/10.1016%2Fj.dnarep.2004.09.012
TI - Solution-state NMR investigation of DNA binding interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): a dynamic description of the DNA/protein interface
T2 - DNA Repair
AU - Buchko, Garry W.
AU - McAteer, Kathleen
AU - Wallace, Susan E.
AU - Kennedy, Michael
PY - 2005
DA - 2005/03/01 00:00:00
PB - Elsevier
SP - 327-339
IS - 3
VL - 4
SN - 1568-7864
ER -
Cite this
BibTex
Copy
@article{2005_Buchko,
author = {Garry W. Buchko and Kathleen McAteer and Susan E. Wallace and Michael Kennedy},
title = {Solution-state NMR investigation of DNA binding interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): a dynamic description of the DNA/protein interface},
journal = {DNA Repair},
year = {2005},
volume = {4},
publisher = {Elsevier},
month = {mar},
url = {https://doi.org/10.1016%2Fj.dnarep.2004.09.012},
number = {3},
pages = {327--339},
doi = {10.1016/j.dnarep.2004.09.012}
}
Cite this
MLA
Copy
Buchko, Garry W., et al. “Solution-state NMR investigation of DNA binding interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): a dynamic description of the DNA/protein interface.” DNA Repair, vol. 4, no. 3, Mar. 2005, pp. 327-339. https://doi.org/10.1016%2Fj.dnarep.2004.09.012.