Common themes in architecture and interactions of prokaryotic PolB2 and Pol V mutasomes inferred from in silico studies
Translesion DNA synthesis (TLS) is typically performed by inherently error-prone Y-family DNA polymerases. Extensively studied Escherichia coli Pol V mutasome, composed of UmuC, an UmuD′ dimer and RecA is an example of a multimeric Y-family TLS polymerase. Less commonly TLS is performed by DNA polym...
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2025-01-01
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| author | Kęstutis Timinskas Albertas Timinskas Česlovas Venclovas |
| author_facet | Kęstutis Timinskas Albertas Timinskas Česlovas Venclovas |
| author_sort | Kęstutis Timinskas |
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| description | Translesion DNA synthesis (TLS) is typically performed by inherently error-prone Y-family DNA polymerases. Extensively studied Escherichia coli Pol V mutasome, composed of UmuC, an UmuD′ dimer and RecA is an example of a multimeric Y-family TLS polymerase. Less commonly TLS is performed by DNA polymerases of other families. One of the most intriguing such cases in B-family is represented by archaeal PolB2 and its bacterial homologs. Previously thought to be catalytically inactive, PolB2 was recently shown to be absolutely required for targeted mutagenesis in Sulfolobus islandicus. However, the composition and structure of the PolB2 holoenzyme remain unknown. We used highly accurate AlphaFold structural models, coupled with protein sequence and genome context analysis to comprehensively characterize PolB2 and its associated proteins, PPB2, a small helical protein, and iRadA, a catalytically inactive Rad51 homolog. We showed that these three proteins can form a heteropentameric PolB2 complex featuring high confidence modeling scores. Unexpectedly, we found that PolB2 binds iRadA through a structural motif reminiscent of RadA/Rad51 oligomerization motif. In some mutasomes we identified clamp binding motifs, present in either iRadA or PolB2, but rarely in both. We also used AlphaFold to derive a three-dimensional structure of Pol V, for which the experimental structure remains unsolved thus precluding comprehensive understanding of its molecular mechanism. Our analysis showed that the structural features of Pol V explain many of the puzzling previous experimental results. Even though models of PolB2 and Pol V mutasomes are structurally different, we found striking similarities in their architectural organization and interactions. |
| format | Article |
| id | doaj-art-bc5c297ecf8b4cff983c3240030fbb9a |
| institution | Kabale University |
| issn | 2001-0370 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj-art-bc5c297ecf8b4cff983c3240030fbb9a2025-01-22T05:41:40ZengElsevierComputational and Structural Biotechnology Journal2001-03702025-01-0127401410Common themes in architecture and interactions of prokaryotic PolB2 and Pol V mutasomes inferred from in silico studiesKęstutis Timinskas0Albertas Timinskas1Česlovas Venclovas2Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, LithuaniaInstitute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, LithuaniaCorresponding author.; Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, LithuaniaTranslesion DNA synthesis (TLS) is typically performed by inherently error-prone Y-family DNA polymerases. Extensively studied Escherichia coli Pol V mutasome, composed of UmuC, an UmuD′ dimer and RecA is an example of a multimeric Y-family TLS polymerase. Less commonly TLS is performed by DNA polymerases of other families. One of the most intriguing such cases in B-family is represented by archaeal PolB2 and its bacterial homologs. Previously thought to be catalytically inactive, PolB2 was recently shown to be absolutely required for targeted mutagenesis in Sulfolobus islandicus. However, the composition and structure of the PolB2 holoenzyme remain unknown. We used highly accurate AlphaFold structural models, coupled with protein sequence and genome context analysis to comprehensively characterize PolB2 and its associated proteins, PPB2, a small helical protein, and iRadA, a catalytically inactive Rad51 homolog. We showed that these three proteins can form a heteropentameric PolB2 complex featuring high confidence modeling scores. Unexpectedly, we found that PolB2 binds iRadA through a structural motif reminiscent of RadA/Rad51 oligomerization motif. In some mutasomes we identified clamp binding motifs, present in either iRadA or PolB2, but rarely in both. We also used AlphaFold to derive a three-dimensional structure of Pol V, for which the experimental structure remains unsolved thus precluding comprehensive understanding of its molecular mechanism. Our analysis showed that the structural features of Pol V explain many of the puzzling previous experimental results. Even though models of PolB2 and Pol V mutasomes are structurally different, we found striking similarities in their architectural organization and interactions.http://www.sciencedirect.com/science/article/pii/S2001037025000108DNA polymerasesTranslesion DNA synthesisRad51RecASequence analysisAlphaFold structural models |
| spellingShingle | Kęstutis Timinskas Albertas Timinskas Česlovas Venclovas Common themes in architecture and interactions of prokaryotic PolB2 and Pol V mutasomes inferred from in silico studies Computational and Structural Biotechnology Journal DNA polymerases Translesion DNA synthesis Rad51 RecA Sequence analysis AlphaFold structural models |
| title | Common themes in architecture and interactions of prokaryotic PolB2 and Pol V mutasomes inferred from in silico studies |
| title_full | Common themes in architecture and interactions of prokaryotic PolB2 and Pol V mutasomes inferred from in silico studies |
| title_fullStr | Common themes in architecture and interactions of prokaryotic PolB2 and Pol V mutasomes inferred from in silico studies |
| title_full_unstemmed | Common themes in architecture and interactions of prokaryotic PolB2 and Pol V mutasomes inferred from in silico studies |
| title_short | Common themes in architecture and interactions of prokaryotic PolB2 and Pol V mutasomes inferred from in silico studies |
| title_sort | common themes in architecture and interactions of prokaryotic polb2 and pol v mutasomes inferred from in silico studies |
| topic | DNA polymerases Translesion DNA synthesis Rad51 RecA Sequence analysis AlphaFold structural models |
| url | http://www.sciencedirect.com/science/article/pii/S2001037025000108 |
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