Molecular Architecture and Functional Dynamics of the Pre-Incision Complex in Nucleotide Excision Repair

Authors

Jina Yu
Chunli Yan
Tanmoy Paul
Lucas Brewer
Susan E Tsutakawa
Chi-Lin Tsai
Samir M Hamdan
John A Tainer
Ivaylo Ivanov

Publication Date

10-1-2024

Journal

Nature Communications

Abstract

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.

Keywords

DNA Repair, DNA-Binding Proteins, Humans, Endonucleases, Transcription Factor TFIIH, Xeroderma Pigmentosum Group D Protein, Cryoelectron Microscopy, Xeroderma Pigmentosum Group A Protein, Transcription Factors, Protein Binding, DNA, Replication Protein A, Models, Molecular, DNA, Single-Stranded, Excision Repair, Nuclear Proteins

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Associated Data

PMID: 39353945