NABP1

NABP1 (hSSB2/OBFC2A) is a nuclear single-stranded DNA-binding protein that safeguards genomic integrity during replication stress and UV-induced DNA damage. Its N-terminal OB-fold domain engages ssDNA and cyclobutane pyrimidine dimers through four key aromatic residues (W59, Y78, W82, Y89), while its C-terminal intrinsically disordered region drives multimerization on ssDNA and liquid-liquid phase separation that concentrates genome-maintenance factors (PMID:26550690, PMID:31443132, PMID:38511671). In the nucleotide excision repair pathway, NABP1 is rapidly recruited to chromatin after UV irradiation and is required for RPA and XPC accumulation at damage sites (PMID:34642383). NABP1 acts redundantly with its paralog SSB1 (NABP2) to protect replication forks and CpG-island integrity; combined loss in hematopoietic and B cell precursors causes massive DNA breakage, R-loop accumulation, and p53-dependent apoptosis (PMID:28270450, PMID:31085591).

1. 2006 Medium

   Establishing NABP1 as a nuclear ssDNA-binding protein resolved its basic biochemical identity: it contains an OB-fold, resides in the nucleus within a high-molecular-mass complex, and preferentially binds single-stranded nucleic acids.

   Evidence Confocal microscopy, size-exclusion chromatography, and nucleic acid binding assays in human cells

   PMID:16533169

   Open questions at the time

   • Identity of high-molecular-mass complex partners unknown
   • No functional assay linking ssDNA binding to a cellular process
2. 2015 High

   Biochemical dissection showed that the C-terminal tail is required for high-affinity ssDNA binding and multimerization, distinguishing NABP1 from NABP2 in substrate preference; meanwhile, single Ssb2-knockout mice revealed functional redundancy with SSB1 in DNA repair.

   Evidence EMSA, ITC, sucrose gradient centrifugation, and Ssb2 knockout mouse model with DNA damage sensitivity assays

   PMID:25917330 PMID:26550690

   Open questions at the time

   • Whether C-terminal tail mediates protein-protein interactions in vivo was untested
   • Extent of SSB1 compensation was not quantitatively defined
3. 2017 High

   NMR mapping identified the ssDNA-binding interface on the OB domain, and double-knockout studies demonstrated that SSB1 and SSB2 cooperate non-redundantly in hematopoietic stem cells to protect replication forks and prevent catastrophic DNA damage.

   Evidence NMR chemical shift perturbation mapping; conditional SSB1/SSB2 double-knockout mice with replication fork dynamics, genome-wide DSB mapping, R-loop detection, and p53 rescue

   PMID:28270450 PMID:29063999

   Open questions at the time

   • Structural basis of OB-fold specificity versus SSB1 not resolved at atomic level
   • Mechanism by which loss of SSBs leads to R-loop accumulation was unclear
4. 2019 High

   The OB domain was shown to directly recognize UV-induced CPD lesions via the same four aromatic residues used for ssDNA binding, providing a structural rationale for NABP1's role in UV damage sensing; double-knockout B cell studies confirmed that ssDNA-binding activity is essential for genome protection.

   Evidence Biolayer interferometry and NMR with CPD-containing substrates; double-knockout B cell precursors with WT and mutant rescue constructs

   PMID:31085591 PMID:31443132

   Open questions at the time

   • Whether CPD recognition occurs on genomic DNA in vivo was not shown
   • Structural model of OB-fold bound to CPD-containing ssDNA was not determined
5. 2021 High

   Placing NABP1 upstream of RPA and XPC in the nucleotide excision repair pathway answered how UV damage recognition translates to repair factor loading: NABP1 depletion impaired RPA32 phosphorylation and XPC recruitment, increasing UV sensitivity.

   Evidence siRNA knockdown in human cells with immunofluorescence, chromatin fractionation, and UVB sensitivity assays

   PMID:34642383

   Open questions at the time

   • Whether NABP1 directly hands off ssDNA to RPA or acts through an intermediary is unknown
   • Relationship between NABP1's CPD binding and RPA recruitment was not mechanistically connected
6. 2024 Medium

   Discovery that NABP1 undergoes liquid-liquid phase separation via its C-terminal IDR provided a biophysical framework for how it concentrates genome-maintenance factors at damage sites.

   Evidence In vitro LLPS reconstitution with IDR deletion mutants and protein enrichment analysis

   PMID:38511671

   Open questions at the time

   • LLPS not demonstrated in cells or at DNA damage foci
   • Functional consequence of phase separation for repair efficiency untested
   • Single-lab observation awaiting independent confirmation
7. 2025 Medium

   Identification of ZC3H13-mediated m6A modification as a stabilizer of NABP1 mRNA linked epitranscriptomic regulation to NABP1's role in cisplatin-induced cell cycle arrest and apoptosis in renal tubular cells.

   Evidence MeRIP, mRNA stability assays, ZC3H13 knockdown/overexpression, and AAV9-mediated silencing in mouse kidneys

   PMID:39985591

   Open questions at the time

   • Whether m6A-mediated regulation of NABP1 operates in other DNA-damage contexts is unknown
   • Direct link between NABP1 protein level changes and cisplatin repair outcomes not established

• Key unresolved questions include whether NABP1 phase condensates form at DNA damage sites in vivo, the atomic-resolution structure of the OB-fold bound to CPD-containing ssDNA, and the mechanism by which NABP1 hands off damaged substrates to RPA during NER.
• No in vivo LLPS imaging at damage foci
• No high-resolution co-crystal or cryo-EM structure with CPD substrate
• Hand-off mechanism from NABP1 to RPA is entirely uncharacterized