Congratulations to Leonardo Serafim, first author, and to group alumnus Brad Kossmann on our new preprint on bioRxiv entitled “Orchestrated metal ion repositioning defines the dynamic catalytic strategy of the essential DNA repair nuclease APE1”, a collaboration with John Tainer, Susan Tsutakawa, Sankar Mitra and David Wilson III.

Human AP-endonuclease 1 (APE1) is a central enzyme of base excision repair: it cuts DNA at abasic sites, among the most common lesions in the genome. How it achieves high specificity and efficient catalysis with a single metal ion has been unclear. We report a high-resolution structure of the APE1–DNA Michaelis complex with its physiological Mg²⁺ cofactor. Combining this structure with molecular dynamics and metadynamics simulations, we uncovered a “moving metal ion” mechanism: the Mg²⁺ ion repositions in a coordinated way to trigger a concerted reaction, without forming a pentavalent intermediate.

A previously unrecognized hydrogen-bonding network couples activation of the catalytic water to the movement of the metal ion, two events that occur on opposite sides of the active site. The findings show how enzymes synchronize distant active-site rearrangements with the transition state, and provide a foundation for designing inhibitors of APE1, which is overexpressed in cancer.

Serafim, L. F., Tsutakawa, S. E., Arvai, A. S., Kossmann, B. R., Mantha, A. K., Abbotts, R., Wilson III, D. M., Mitra, S., Tainer, J. A. & Ivanov, I.* bioRxiv 2026.05.11.724140.

Congratulations to Tanmoy Paul, Chunli Yan and Grant Derdeyn-Blackwell who are co-authors on a just published paper in the journal Nature Communications entitled “Translocation mechanism of xeroderma pigmentosum group D protein on single-stranded DNA and genetic disease etiology”. We investigated the molecular basis of translocation by the xeroderma pigmentosum group D (XPD) helicase on single-stranded DNA (ssDNA), a process essential for DNA damage verification in the nucleotide excision repair (NER) pathway. XPD is a 5′–3′ helicase that functions as the motor subunit of the TFIIH complex in NER. XPD’s activity is vital for genome maintenance.

To define its structural mechanism, we combined structure modeling with advanced simulations, including chain-of-replicas path optimization, transition path sampling, and Markov state modeling. These methods allowed us to characterize the conformational ensembles of apo, ADP-bound, and ATP-bound XPD and map the full free energy landscape of its ATPase cycle. Our analysis uncovered two distinct constrictions along the path of ssDNA located at the opposite ends of the DNA-binding groove. These function as alternating clamps that capture and release ssDNA in a coordinated manner. DNA translocation results from the dynamic interplay of the motor domains and the two constrictions. We establish a novel structural relationship between the movement of the XPD motor domains (RecA1 and RecA2) and the reciprocal rearrangement of the Arch domain, mediated by hydrophobic interactions involving the spring helix of RecA2 and the Arch domain. This coordinated conformational switching of XPD’s domains resembles the mechanism seen in SF1B helicases. Notably, the posited mechanism differs from the scaffold inversion strategy used by SF1A enzymes.

Impairment of NER by mutations causes severe human genetic disorders, highlighting the need for molecular-level understanding of XPD’s function. We therefore examined the functional  impacts of XPD-associated disease mutations and found that many cluster in regions essential for DNA engagement and conformational switching during translocation. Mutations that weaken ssDNA binding correlate with the cancer-prone xeroderma pigmentosum phenotype, while those disrupting helicase-core flexibility are linked to XP/Cockayne syndrome. Mutations positioned outside the DNA groove commonly underlie trichothiodystrophy due to impaired TFIIH interactions.

Congratulations to Tanmoy Paul, Chunli Yan and Jina Yu who are co-authors on a just published paper in the journal Nature Communications. The paper is entitled “Molecular model of TFIIH recruitment to the transcription-coupled repair machinery“. Transcription-coupled repair is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of the CSB protein to lesion-stalled RNA polymerase II (Pol II) initiates the pathway by triggering the recruitment of downstream repair factors. Despite recent cryo-EM advances, it remains unknown how one such factor – transcription factor IIH (TFIIH) – is recruited to the intact transcription-coupled repair complex. Combining existing structural data with AlphaFold predictions, we built an integrative model of the initial TFIIH-bound complex and used large-scale molecular simulations to unveil its structural dynamics. We show how TFIIH can be first recruited in an open repair-inhibited conformation, which requires subsequent CAK kinase module removal and conformational closure to process damaged DNA. Collectively, our findings elucidate the coordinated assembly of repair proteins in early transcription-coupled repair.

Congratulations to Jina Yu, Chunli Yan, Tanmoy Paul and Lucas Brewer who are co-authors on a just published paper in the journal Nature Communications. The paper is entitled “Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair.” The nucleotide excision repair (NER) pathway is vital for genome integrity. By synthesizing cryo-EM and XL-MS data with computational modeling and AlphaFold2 predictions, we elucidate the structure and dynamics of a critically important state of the NER machinery – the pre-incision complex (PInC). Our analyses yield key mechanistic insights into PInC’s assembly and regulation, the structural basis of XPF and XPG nuclease coordination, and the licensing of the NER dual incision. Using graph-theoretical algorithms, we moreover build dynamic network models of the PInC, which powerfully elucidate the etiology of devastating human genetic syndromes.