Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain
Abstract
:1. Introduction
2. Results and Discussion
2.1. Prediction of New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to the Experimentally Validated Zα Domain
2.2. Domain Composition and Nuclear Localisation Signals within the Most Promising Z-DNA/Z-RNA Binding Proteins
2.3. Representative Molecular Docking of RPA2 Region Structurally Similar to Zα Domain and Z-DNA/Z-RNA
2.4. Functional Enrichment and Interaction Network of Human Z-DNA/Z-RNA Binding Proteins
3. Materials and Methods
3.1. Collection of Experimentally-Validated Z-DNA/RNA Binding Protein Structures
3.2. Structure-Based Similarity Searches
3.3. Structure Visualisation and Contacts/Clashes Depicting
3.4. Structural Alignment Construction
3.5. Docking to Z-DNA/RNA
3.6. Functional Enrichment Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Protein Symbol/ID | Protein Name | Organism | Protein Length | Function | PDB ID | Method/ Resolution | Domain | Ref. |
---|---|---|---|---|---|---|---|---|
ADAR (P55265) | Double-stranded RNA-specific adenosine deaminase | Homo sapiens | 1226 | Hydrolytic deamination of adenosine to inosine in dsRNA (A-to-I RNA editing) | 1XMK | XRC/0.97 Å | Zβ | [60] |
1QGP | NMR | Zα | [61] | |||||
3F21 | XRC/2.20 Å | Zα | [58] | |||||
3F22 | XRC/2.50 Å | Zα | ||||||
3F23 | XRC/2.70 Å | Zα | ||||||
2GXB | XRC/2.25 Å | Zα | [16] | |||||
ZBP1 (Q9H171) | Z-DNA-binding protein 1 | Homo sapiens | 429 | Innate sensor recognising viral Z-RNA | 2L4M | NMR | Zβ | [62] |
Zbp1/DAI | Z-DNA-binding protein 1 | Mus musculus | 411 | 1J75 | XRC/1.85 Å | Zα | [18] | |
PKZ (Q5NE12) | Protein kinase-containing Z-DNA-binding domains | Danio rerio | 511 | Defence response to virus | 4LB5 | XRC/2.00 Å | Zα | [20] |
4LB6 | XRC/1.80 Å | |||||||
ORF112 (A4FTK7) | Protein ORF112 | Cyprinid herpesvirus 3 | 278 | Double-stranded RNA adenosine deaminase activity; RNA binding | 4WCG | XRC/1.50 Å | Zα | [21] |
E3L (P21605) | Protein E3 | Vaccinia virus | 190 | Double-stranded RNA adenosine deaminase activity; inhibition of multiple cellular antiviral responses activated by dsRNA | 7C0I | XRC/2.40 Å | Zα | [63] |
34L (Q9DHS8) | 34L protein | Yaba-like disease virus | 185 | Same as E3L | 1SFU | XRC/2.00 Å | Zα | [22] |
Protein Symbol/ID | Protein Name | Organism | Domain | Protein Length | Cellular Localisation/Known Function |
---|---|---|---|---|---|
HOP2 (O35047) | Homologous-pairing protein 2 homolog | Mus musculus | Eukarya | 217 | Nucleus/DNA binding, meiotic recombination, double-strand break repair, positive regulation of transcription by RNA pol II [65,66] |
DsvD (Q46582) | DsvD | Desulfovibrio vulgaris | Bacteria | 78 | Role in dissimilatory sulfite reduction, Possible Interaction with B- and Z-DNA by Its Winged-Helix Motif [67] |
D2PEW5 | Uncharacterised DNA binding protein | Sulfolobus islandicus | Archaea | 59 | DNA binding |
feoC (B5XTS6) | Probable [Fe-S]-dependent transcriptional repressor | Klebsiella pneumoniae | Bacteria | 79 | DNA binding may function as a transcriptional regulator that controls feoABC expression [68] |
pefI (Q04822) | FaeA-like protein | Salmonella typhimurium | Bacteria | 70 | Regulation of transcription [69] |
RPA2 (P15927) | Replication protein A 32 kDa subunit | Homo sapiens | Eukarya | 270 | Nucleus/DNA binding, multifunctional protein (DNA repairs, DNA replication, telomere maintenance, preventing G-quadruplex formation) [70,71,72,73] |
CDC53 (Q12018) | Cell division control protein 53 | Saccharomyces cerevisiae | Eukarya | 815 | Nucleus & Cytoplasm/DNA replication origin binding, cell division, protein ubiquitination [74] |
CUL1 (Q13616) | Cullin-1 | Homo sapiens | Eukarya | 776 | Nucleus & Cytoplasm/Protein ubiquitination, cell division, transcription regulation [75] |
ANC2 (Q9UJX6) | Anaphase-promoting complex subunit 2 | Homo sapiens | Eukarya | 822 | Nucleus & Cytoplasm/Component of the anaphase promoting complex/cyclosome (APC/C) [76] |
SCC1 (Q12158) | Sister chromatid cohesion protein 1 | Saccharomyces cerevisiae | Eukarya | 566 | Nucleus/Mitotic sister chromatid cohesion, double-strand break repair [77] |
APC2 (Q12440) | Anaphase-promoting complex subunit 2 | Saccharomyces cerevisiae | Eukarya | 853 | Nucleus & cytoplasm/Component of the anaphase promoting complex/cyclosome (APC/C) [78] |
Rpc34 (Q921X6) | DNA-directed RNA polymerase III subunit RPC6 | Mus musculus | Eukarya | 316 | Nucleus/Nuclear and cytosolic DNA sensor involved in innate immune response, defence response to the virus [79] |
PBP2 (A0A0E3GTJ4) | Archaeal DNA polymerase holoenzyme (PBP2 subunit) | Saccharolobus solfataricus | Archaea | 76 | Enhances DNA synthesis [80] |
Reut_B4095 (Q46TT3) | Putative DNA-binding protein | Cupriavidus pinatubonensis | Bacteria | 95 | DNA binding |
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Bartas, M.; Slychko, K.; Brázda, V.; Červeň, J.; Beaudoin, C.A.; Blundell, T.L.; Pečinka, P. Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain. Int. J. Mol. Sci. 2022, 23, 768. https://doi.org/10.3390/ijms23020768
Bartas M, Slychko K, Brázda V, Červeň J, Beaudoin CA, Blundell TL, Pečinka P. Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain. International Journal of Molecular Sciences. 2022; 23(2):768. https://doi.org/10.3390/ijms23020768
Chicago/Turabian StyleBartas, Martin, Kristyna Slychko, Václav Brázda, Jiří Červeň, Christopher A. Beaudoin, Tom L. Blundell, and Petr Pečinka. 2022. "Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain" International Journal of Molecular Sciences 23, no. 2: 768. https://doi.org/10.3390/ijms23020768