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Cited by 84DNA Repair MechanismsProtein Structure and DynamicsEnzyme Structure and Function

Interactions of Human Nucleotide Excision Repair Protein XPA with DNA and RPA70ΔC327: Chemical Shift Mapping and 15N NMR Relaxation Studies

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Buchko, Garry W., Daughdrill, Gary W., de Lorimier, Robert, Sudha Rao B. K.,, Isern, Nancy G., Lingbeck, Jody M., Taylor, John-Stephen, Wold, Marc S. +4 more·1999·Biochemistry
DOI 10.1021/bi991755pPMC PMC4251892
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Abstract

Human XPA is an essential component in the multienzyme nucleotide excision repair (NER) pathway. The solution structure of the minimal DNA binding domain of XPA (XPA-MBD: M98-F219) was recently determined [Buchko et al. (1998) Nucleic Acids Res. 26, 2779-2788, Ikegami et al. (1998) Nat. Struct. Biol. 5, 701-706] and shown to consist of a compact zinc-binding core and a loop-rich C-terminal subdomain connected by a linker sequence. Here, the solution structure of XPA-MBD was further refined using an entirely new class of restraints based on pseudocontact shifts measured in cobalt-substituted XPA-MBD. Using this structure, the surface of XPA-MBD which interacts with DNA and a fragment of the largest subunit of replication protein A (RPA70 Delta C327: M1-Y326) was determined using chemical shift mapping. DNA binding in XPA-MBD was highly localized in the loop-rich subdomain for DNA with or without a lesion [dihydrothymidine (dhT) or 6-4-thymidine-cytidine (64TC)], or with DNA in single- or double-stranded form, indicating that the character of the lesion itself is not the driving force for XPA binding DNA. RPA70 Delta C327 was found to contact regions in both the zinc-binding and loop-rich subdomains. Some overlap of the DNA and RPA70 Delta C327 binding regions was observed in the loop-rich subdomain, indicating a possible cooperative DNA-binding mode between XPA and RPA70 Delta C327. To complement the chemical shift mapping data, the backbone dynamics of free XPA-MBD and XPA-MBD bound to DNA oligomers containing dhT or 64TC lesions were investigated using 15N NMR relaxation data. The dynamic analyses for the XPA-MBD complexes with DNA revealed localized increases and decreases in S2 and an increase in the global correlation time. Regions of XPA-MBD with the largest increases in S2 overlapped regions having the largest chemical shifts changes upon binding DNA, indicating that the loop-rich subdomain becomes more rigid upon binding DNA. Interestingly, S2 decreased for some residues in the zinc-binding core upon DNA association, indicating a possible concerted structural rearrangement on binding DNA.

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Authors
Buchko, G. W., Daughdrill, G. W., de Lorimier, R., Sudha Rao B. K., Isern, N. G., Lingbeck, J. M., Taylor, J.-S., Wold, M. S., Gochin, M., Spicer, L. D., Lowry, D. F., & Kennedy, M. A.
Affiliations
  • University of Iowa (US)
  • Pacific Northwest National Laboratories, Environmental Molecular Sciences Laboratory, Richland, Washington 99352, Departments of Biochemistry and Radiology, Duke University Medical Center, Durham, North Carolina 27710, Department of Biochemistry, University of Iowa College of Medicine, Iowa City, Iowa 52240, Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
Corresponding author
Kennedy, Michael A.
ORCID
Venue
Biochemistry
Publisher
American Chemical Society (ACS)
Published
1999-10-27
Volume
38
Issue
46
Pages
15116-15128
ISSN
  • 0006-2960 (ISSN-L)
  • 1520-4995
DOI
10.1021/bi991755p
PMC
PMC4251892
OpenAlex
W2136199465
Cited by
83
References
63
Citations by year
2025: 1 · 2024: 5 · 2023: 1 · 2022: 3 · 2021: 3 · 2020: 3 · 2019: 2 · 2018: 1 · 2017: 9 · 2016: 2 · 2015: 4 · 2014: 5 · 2013: 4
FWCI
1.26
Type
journal article
Language
en
Open access
Locations
  • Biochemistry (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Digital Commons - University of South Florida (University of South Florida) (submittedVersion)
Funders
National Institute of General Medical Sciences (R01GM044721, R29GM053164)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
XPA, nucleotide excision repair, RPA70, DNA binding, DNA lesions, backbone dynamics, 15N relaxation, chemical shift mapping, cooperative DNA binding
MeSH terms
Binding Sites, DNA, DNA Repair, DNA Replication, DNA-Binding Proteins, DNA, Single-Stranded, Humans, Nitrogen Isotopes, Oligodeoxyribonucleotides, Peptide Fragments, Protein Conformation, Solutions, Thermodynamics, RNA-Binding Proteins, Nuclear Magnetic Resonance, Biomolecular, Replication Protein A, Xeroderma Pigmentosum Group A Protein

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