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.