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PreprintCited by 3DNA Repair MechanismsEnzyme Structure and FunctionGenomics and Phylogenetic Studies

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The Rad52 superfamily as seen by AlphaFold

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Al-Fatlawi, Ali, Hossen, Md. Ballal, de Paula Lopes, Stella, Stewart, A. Francis, Schroeder, Michael·2024·Computational and Structural Biotechnology Journal
DOI 10.1101/2024.08.09.607149PMC PMC11783212

Preprint — published as 10.1016/j.csbj.2024.12.012 · Paper page

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Abstract

1 Rad52, a highly conserved eukaryotic protein, plays a crucial role in DNA repair, especially in double-strand break repair. Recent findings reveal that its distinct structural features, including a characteristic β -sheet and β -hairpin motif, are shared with the lambda phage single-strand annealing proteins, Red β , indicating a common superfamily. Our analysis of over 10,000 single-strand annealing proteins (SSAPs) across all kingdoms of life supports this hypothesis, confirming their possession of the characteristic motif despite variations in size and composition. We found that archaea, representing only 1% of the studied proteins, exhibit most of these variations. Through the examination of four representative archaeal SSAPs, we elucidate the structural relationship between eukaryotic and bacterial SSAPs, highlighting differences in β -sheet size and β -hairpin complexity. Furthermore, we identify an archaeal SSAP with a structure nearly identical to the human variant and screen over 100 million unannotated proteins for potential SSAP candidates. Our computational analysis complements existing sequence with structural evidence supporting the suggested orthology among five SSAP families across all kingdoms: Rad52, Red β , RecT, Erf, and Sak3.

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Metadata

Authors
Al-Fatlawi, A., Hossen, M. B., de Paula Lopes, S., Stewart, A. F., & Schroeder, M.
Affiliations
  • Biotechnologisches Zentrum (DE)
  • Center for Scalable Data Analytics and Artificial Intelligence (DE)
Corresponding author
Schroeder, Michael
ORCID
Venue
Computational and Structural Biotechnology Journal
Publisher
openRxiv
Published
2024-08-09
Volume
27
Pages
360-368
ISSN
2001-0370 (ISSN-L)
DOI
10.1101/2024.08.09.607149
PMC
PMC11783212
OpenAlex
W4405761093
Cited by
3
References
1
Citations by year
2026: 2 · 2025: 1
FWCI
0.41
Type
journal article
Language
en
Open access
Licence
Locations
  • Computational and Structural Biotechnology Journal (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Qucosa (Saxon State and University Library Dresden) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • Bundesministerium für Bildung und Forschung
  • Technische Universität Dresden
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
RAD52, protein structure, DNA repair, homologous recombination, ERF

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