Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair

• Published in: Nature communications Vol. 15; no. 1; pp. 8511 - 15
• Main Authors: Yu, Jina, Yan, Chunli, Paul, Tanmoy, Brewer, Lucas, Tsutakawa, Susan E., Tsai, Chi-Lin, Hamdan, Samir M., Tainer, John A., Ivanov, Ivaylo
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.10.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 60 APPLIED LIFE SCIENCES; 631/337/1427/1430; 631/535/1267; Clustering; Cockayne syndrome; Cryoelectron Microscopy; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - genetics; DNA - metabolism; DNA Repair; DNA, Single-Stranded - genetics; DNA, Single-Stranded - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Endonucleases - genetics; Endonucleases - metabolism; ERCC1 protein; Excision Repair; Genetic disorders; Grooves; Humanities and Social Sciences; Humans; Models, Molecular; Molecular modelling; Molecular structure; multidisciplinary; Mutation; Nuclear Proteins; Nucleotide excision repair; Nucleotides; Phenotypes; Protein Binding; Regulatory mechanisms (biology); Replication Protein A - genetics; Replication Protein A - metabolism; Rigging; Science; Science (multidisciplinary); Structural models; Transcription Factor TFIIH - chemistry; Transcription Factor TFIIH - genetics; Transcription Factor TFIIH - metabolism; Transcription Factors - genetics; Transcription Factors - metabolism; Xeroderma pigmentosum; Xeroderma Pigmentosum Group A Protein - genetics; Xeroderma Pigmentosum Group A Protein - metabolism; Xeroderma Pigmentosum Group D Protein - chemistry; Xeroderma Pigmentosum Group D Protein - genetics; Xeroderma Pigmentosum Group D Protein - metabolism; XPD protein
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-52860-y

Nucleotide excision repair (NER) is vital for genome integrity. Yet, our understanding of the complex NER protein machinery remains incomplete. Combining cryo-EM and XL-MS data with AlphaFold2 predictions, we build an integrative model of the NER pre-incision complex(PInC). Here TFIIH serves as a molecular ruler, defining the DNA bubble size and precisely positioning the XPG and XPF nucleases for incision. Using simulations and graph theoretical analyses, we unveil PInC’s assembly, global motions, and partitioning into dynamic communities. Remarkably, XPG caps XPD’s DNA-binding groove and bridges both junctions of the DNA bubble, suggesting a novel coordination mechanism of PInC’s dual incision. XPA rigging interlaces XPF/ERCC1 with RPA, XPD, XPB, and 5′ ssDNA, exposing XPA’s crucial role in licensing the XPF/ERCC1 incision. Mapping disease mutations onto our models reveals clustering into distinct mechanistic classes, elucidating xeroderma pigmentosum and Cockayne syndrome disease etiology. This study unveils the structure, dynamics, and regulatory mechanisms of a key nucleotide excision repair intermediate—the pre-incision complex (PInC). The PInC structural model links positions of disease mutations to genetic disease phenotypes.