User:Julia Takuno Hespanhol/Sandbox 1

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==VRR-Nuc domain==
==VRR-Nuc domain==
<StructureSection load='4QBN' size='340' side='right' caption='VRR-Nuc containing Salmonella phage SETP3 protein' scene=''>
<StructureSection load='4QBN' size='340' side='right' caption='VRR-Nuc containing Salmonella phage SETP3 protein' scene=''>
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[[Image:4qlb com conservados marcado|300px|left|thumb| 4QLB with conserved residues im pink]]
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This is a default text for your page '''Julia Takuno Hespanhol/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
This is a default text for your page '''Julia Takuno Hespanhol/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
You may include any references to papers as in: the use of the phage structure in Proteopedia <ref>DOI:10.1016/j.celrep.2014.06.001</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
You may include any references to papers as in: the use of the phage structure in Proteopedia <ref>DOI:10.1016/j.celrep.2014.06.001</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
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== Structural Highlights==
== Structural Highlights==
The VRR-Nuc containing proteins, since belonging to the PD(D/E)xK superfamily, present structure similar to the core structure of the superfamily. The conserved core includes αβββαβ, in which the conserved residues responsible for the nuclease activity D (Aspartic Acid), D/E (Glutamic Acid), K (Lysine) are usually found in the second and third β-sheets. The Aspartic and Glutamic Acid residues coordinates metal atoms, while the Lysine residue associates with a water molecule to attack the phosphodiester bond. The α-helixes are usually associated to substrate binding and enzyme dimerization and stabilization. <ref>doi:10.1093/nar/gks382</ref><ref>doi:10.1111/febs.15870</ref>
The VRR-Nuc containing proteins, since belonging to the PD(D/E)xK superfamily, present structure similar to the core structure of the superfamily. The conserved core includes αβββαβ, in which the conserved residues responsible for the nuclease activity D (Aspartic Acid), D/E (Glutamic Acid), K (Lysine) are usually found in the second and third β-sheets. The Aspartic and Glutamic Acid residues coordinates metal atoms, while the Lysine residue associates with a water molecule to attack the phosphodiester bond. The α-helixes are usually associated to substrate binding and enzyme dimerization and stabilization. <ref>doi:10.1093/nar/gks382</ref><ref>doi:10.1111/febs.15870</ref>
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[[Image:4qlb com conservados marcado|300px|left|thumb| 4QLB with conserved residues im pink]]
The VRR-Nuc containing proteins might present a single domain, only the VRR-Nuc domain <ref>doi:10.1016/j.celrep.2014.06.001</ref>, or present other domains, such as the human FAN1 (human FANCD2-associasted nuclease) <ref>DOI: 10.3233/JHD-200448</ref> and its homologues <ref>DOI: DOI:10.1101/gad.248492.114</ref>. The human FAN1 is composed by 4 well conserved domains: UBZ (ubiquitin-binding zinc finger), which participates in substrate recognition and binding; SAP (SAF-A/B, Acinus and PIAS) related to DNA binding; TRP (tetratricopeptide repeat) implicated in FAN1 dimerization and protein-protein interactions; and the VRR-Nuc catalytic domain. <ref>DOI: 10.3233/JHD-200448</ref>
The VRR-Nuc containing proteins might present a single domain, only the VRR-Nuc domain <ref>doi:10.1016/j.celrep.2014.06.001</ref>, or present other domains, such as the human FAN1 (human FANCD2-associasted nuclease) <ref>DOI: 10.3233/JHD-200448</ref> and its homologues <ref>DOI: DOI:10.1101/gad.248492.114</ref>. The human FAN1 is composed by 4 well conserved domains: UBZ (ubiquitin-binding zinc finger), which participates in substrate recognition and binding; SAP (SAF-A/B, Acinus and PIAS) related to DNA binding; TRP (tetratricopeptide repeat) implicated in FAN1 dimerization and protein-protein interactions; and the VRR-Nuc catalytic domain. <ref>DOI: 10.3233/JHD-200448</ref>

Revision as of 17:03, 10 December 2021

VRR-Nuc domain

VRR-Nuc containing Salmonella phage SETP3 protein

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References

  1. ↑ Pennell S, Declais AC, Li J, Haire LF, Berg W, Saldanha JW, Taylor IA, Rouse J, Lilley DM, Smerdon SJ. FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain. Cell Rep. 2014 Jul 10;8(1):84-93. doi: 10.1016/j.celrep.2014.06.001. Epub 2014, Jun 26. PMID:24981866 doi:http://dx.doi.org/10.1016/j.celrep.2014.06.001
  2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
  3. ↑ Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Nucleic Acids Res. 2012 Aug;40(15):7016-45. doi: 10.1093/nar/gks382. Epub 2012, May 25. PMID:22638584 doi:http://dx.doi.org/10.1093/nar/gks382
  4. ↑ Wang S, Geng Z, Zhang H, She Z, Dong Y. The Pseudomonas aeruginosa PAAR2 cluster encodes a putative VRR-NUC domain-containing effector. FEBS J. 2021 Apr 10. doi: 10.1111/febs.15870. PMID:33838074 doi:http://dx.doi.org/10.1111/febs.15870
  5. ↑ Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Nucleic Acids Res. 2012 Aug;40(15):7016-45. doi: 10.1093/nar/gks382. Epub 2012, May 25. PMID:22638584 doi:http://dx.doi.org/10.1093/nar/gks382
  6. ↑ Wang S, Geng Z, Zhang H, She Z, Dong Y. The Pseudomonas aeruginosa PAAR2 cluster encodes a putative VRR-NUC domain-containing effector. FEBS J. 2021 Apr 10. doi: 10.1111/febs.15870. PMID:33838074 doi:http://dx.doi.org/10.1111/febs.15870
  7. ↑ Pennell S, Declais AC, Li J, Haire LF, Berg W, Saldanha JW, Taylor IA, Rouse J, Lilley DM, Smerdon SJ. FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain. Cell Rep. 2014 Jul 10;8(1):84-93. doi: 10.1016/j.celrep.2014.06.001. Epub 2014, Jun 26. PMID:24981866 doi:http://dx.doi.org/10.1016/j.celrep.2014.06.001
  8. ↑ Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis. 2021;10(1):95-122. doi: 10.3233/JHD-200448. PMID:33579867 doi:http://dx.doi.org/10.3233/JHD-200448
  9. ↑ Arav VI, Slesarev SM, Slesareva EV. A method for extirpation of the pineal gland in albino rats. Bull Exp Biol Med. 2008 Sep;146(3):382-4. PMID:19240866 doi:doi
  10. ↑ Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis. 2021;10(1):95-122. doi: 10.3233/JHD-200448. PMID:33579867 doi:http://dx.doi.org/10.3233/JHD-200448
  11. ↑ 10.1016/j.celrep.2014.06.001
  12. ↑ 10.1016/j.celrep.2014.06.001
  13. ↑ Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis. 2021;10(1):95-122. doi: 10.3233/JHD-200448. PMID:33579867 doi:http://dx.doi.org/10.3233/JHD-200448
  14. ↑ Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis. 2021;10(1):95-122. doi: 10.3233/JHD-200448. PMID:33579867 doi:http://dx.doi.org/10.3233/JHD-200448
  15. ↑ Deans AJ, West SC. DNA interstrand crosslink repair and cancer. Nat Rev Cancer. 2011 Jun 24;11(7):467-80. doi: 10.1038/nrc3088. PMID:21701511 doi:http://dx.doi.org/10.1038/nrc3088
  16. ↑ Deans AJ, West SC. DNA interstrand crosslink repair and cancer. Nat Rev Cancer. 2011 Jun 24;11(7):467-80. doi: 10.1038/nrc3088. PMID:21701511 doi:http://dx.doi.org/10.1038/nrc3088
  17. ↑ Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis. 2021;10(1):95-122. doi: 10.3233/JHD-200448. PMID:33579867 doi:http://dx.doi.org/10.3233/JHD-200448
  18. ↑ Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis. 2021;10(1):95-122. doi: 10.3233/JHD-200448. PMID:33579867 doi:http://dx.doi.org/10.3233/JHD-200448
  19. ↑ Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis. 2021;10(1):95-122. doi: 10.3233/JHD-200448. PMID:33579867 doi:http://dx.doi.org/10.3233/JHD-200448

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