# Unveiling nuclear localization signals in human arginine deiminase proteins

**Authors:** José L. Neira, Olga Abian, Adrián Velazquez‐Campoy, Bruno Rizzuti

PMC · DOI: 10.1002/pro.70517 · Protein Science : A Publication of the Protein Society · 2026-03-02

## TL;DR

This study identifies nuclear localization signals in three human arginine deiminase enzymes and shows they can bind to importin proteins, suggesting they can enter the cell nucleus.

## Contribution

The study experimentally validates predicted nuclear localization signals in PADI1, PADI2, and PADI3 and demonstrates their binding to importin α3.

## Key findings

- The predicted NLSs in PADI1, PADI2, and PADI3 were confirmed to bind to importin α3 and its truncated form.
- The isolated peptides were disordered and monomeric in solution but showed low micromolar binding affinity.
- The NLSs target the canonical importin binding site, suggesting a role in nuclear translocation of PADI enzymes.

## Abstract

Arginine iminohydrolases are a family of enzymes involved in the conversion of arginine to citrulline. There are five isoforms in humans (PADI1, 2, 3, 4, and 6). Some of them are observed experimentally in the cytoplasm and in the nucleus of the cell; for moving to the latter location, they must pass through the cell nuclear membrane by using the translocation machinery, mainly formed by the proteins named importins. We have previously described and characterized the isolated PADI4 nuclear localization sequences (NLSs) and their binding to importin α3 (Impα3). By using theoretical predictors, here we foretold the existence of several NLSs in isoforms PADI1, PADI2, and PADI3. These predicted polypeptide regions were chemically synthesized, and the soluble ones were conformationally characterized in isolation. We studied their ability to bind Impα3 and its truncated species (ΔImpα3) without the importin binding domain, by using several biophysical techniques and molecular simulations. The isolated peptides were disordered and monomeric in solution. Moreover, all of them were capable of binding to both importin species with affinities in the low micromolar range, and targeting the canonical NLS binding site for cargo proteins. These findings suggest that the predicted NLS regions could be the sites for the binding of the corresponding intact PADI protein to importin, and therefore, any of the PADI enzymes could be translocated into the nucleus.

## Linked entities

- **Genes:** PADI1 (peptidyl arginine deiminase 1) [NCBI Gene 29943], PADI2 (peptidyl arginine deiminase 2) [NCBI Gene 11240], PADI3 (peptidyl arginine deiminase 3) [NCBI Gene 51702], PADI4 (peptidyl arginine deiminase 4) [NCBI Gene 23569], PADI6 (peptidyl arginine deiminase 6) [NCBI Gene 353238]
- **Proteins:** BPNT2 (3'(2'), 5'-bisphosphate nucleotidase 2)

## Full-text entities

- **Genes:** PADI2 (peptidyl arginine deiminase 2) [NCBI Gene 11240] {aka PAD-H19, PAD2, PDI2}, KPNA3 (karyopherin subunit alpha 3) [NCBI Gene 3839] {aka IPOA4, SPG88, SRP1, SRP1gamma, SRP4, hSRP1}, PADI6 (peptidyl arginine deiminase 6) [NCBI Gene 353238] {aka OZEMA16, PREMBL2, hPADVI}, RAN (RAN, member RAS oncogene family) [NCBI Gene 5901] {aka ARA24, Gsp1, TC4}, PADI3 (peptidyl arginine deiminase 3) [NCBI Gene 51702] {aka PAD3, PDI3, UHS1}, NSL1 (NSL1 component of MIS12 kinetochore complex) [NCBI Gene 25936] {aka C1orf48, DC8, MIS14}, PSAT1 (phosphoserine aminotransferase 1) [NCBI Gene 29968] {aka EPIP, NLS2, PSA, PSAT, PSATD}, PHGDH (phosphoglycerate dehydrogenase) [NCBI Gene 26227] {aka 3-PGDH, 3PGDH, HEL-S-113, NLS, NLS1, PDG}, KPNA1 (karyopherin subunit alpha 1) [NCBI Gene 3836] {aka IPOA5, NPI-1, RCH2, SRP1}, NPC1 (NPC intracellular cholesterol transporter 1) [NCBI Gene 4864] {aka NPC, POGZ, SLC65A1}, RANBP3 (RAN binding protein 3) [NCBI Gene 8498], PADI4 (peptidyl arginine deiminase 4) [NCBI Gene 23569] {aka PAD, PAD4, PADI5, PDI4, PDI5}, PADI1 (peptidyl arginine deiminase 1) [NCBI Gene 29943] {aka HPAD10, PAD1, PDI, PDI1}, BPNT2 (3'(2'), 5'-bisphosphate nucleotidase 2) [NCBI Gene 54928] {aka GPAPP, IMP 3, IMP-3, IMPA3, IMPAD1}
- **Diseases:** rheumatoid arthritis (MESH:D001172), multiple sclerosis (MESH:D009103), Alzheimer's disease (MESH:D000544), cancer (MESH:D009369), inflammation (MESH:D007249), psoriasis (MESH:D011565)
- **Chemicals:** phenylalanines (MESH:D010649), arginine (MESH:D001120), 1H (-), dioxane (MESH:C025223), sodium phosphate (MESH:C018279), disulfide (MESH:D004220), tryptophan (MESH:D014364), Ampicillin (MESH:D000667), His (MESH:D006639), Triton X-100 (MESH:D017830), methanol (MESH:D000432), NaCl (MESH:D012965), (+)-10-camphorsulfonic acid (MESH:C006881), phosphate (MESH:D010710), citrulline (MESH:D002956), SDS (MESH:D012967), D2O. (MESH:D017666), Water (MESH:D014867), Imidazole (MESH:C029899), tyrosine (MESH:D014443), peptides (MESH:D010455)
- **Species:** Homo sapiens (human, species) [taxon 9606]
- **Mutations:** Ser546, Cys564Ser, Cys546, Ser564, Cys564, Cys546Ser

## Full text

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## Figures

9 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12953195/full.md

## References

87 references — full list in the complete paper: https://tomesphere.com/paper/PMC12953195/full.md

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Source: https://tomesphere.com/paper/PMC12953195