Biology:Macro domain

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Macro
PDB 1zr3 EBI.jpg
Crystal structure of the macro-domain of human core histone variant macroh2a1.1
Identifiers
SymbolMacro
PfamPF01661
Pfam clanCL0223
InterProIPR002589
SCOP21vhu / SCOPe / SUPFAM
CDDcd02749

In molecular biology, the Macro domain (often also written macrodomain) or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose, an NAD metabolite, or related ligands. Binding to ADP-ribose can be either covalent or non-covalent:[1] in certain cases it is believed to bind non-covalently,[2] while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein.[3]

Function

The domain was described originally in association with the ADP-ribose 1-phosphate (Appr-1-P)-processing activity (A1pp) of the yeast YBR022W protein and called A1pp.[4] However, the domain has been renamed Macro as it is the C-terminal domain of mammalian core histone macro-H2A.[5][6] Macro domain proteins can be found in eukaryotes, in (mostly pathogenic) bacteria, in archaea and in ssRNA viruses, such as coronaviruses, Rubella and Hepatitis E viruses. In vertebrates the domain occurs in e.g. histone macroH2A, predicted poly-ADP-ribose polymerases (PARPs) and B aggressive lymphoma (BAL) protein.

ADP-ribosylation of proteins is an important post-translational modification that occurs in a variety of biological processes, including DNA repair, regulation of transcription, chromatin biology, maintenance of genomic stability, telomere dynamics,[7] cell differentiation and proliferation,[8] necrosis and apoptosis,[9] and long-term memory formation.[10] The Macro domain recognises the ADP-ribose nucleotide and in some cases poly-ADP-ribose, and is thus a high-affinity ADP-ribose-binding module found in a number of otherwise unrelated proteins.[11] ADP-ribosylation of DNA is relatively uncommon and has only been described for a small number of toxins that include pierisin,[12] scabin[13] and DarT.[14][15] The Macro domain from the antitoxin DarG of the toxin-antitoxin system DarTG, both binds and removes the ADP-ribose modification added to DNA by the toxin DarT.[14][15] The Macro domain from human, macroH2A1.1, binds an NAD metabolite O-acetyl-ADP-ribose.[16]

Class Subclass Species Activity
MacroH2A-like e ADP-ribose binding
MacroD-type ‘classic’ a, b, e, v ADP-ribosyl bond hydrolysis
Zn-dependent b, e ADP-ribosyl bond hydrolysis
GDAP2-like e ADP-ribose binding
ALC1-like b, e ADP-ribose binding or ADP-ribosyl bond hydrolysis
PARG-like PARG_cat e ADP-ribosyl bond hydrolysis
mPARG (DUF2263) b, e, v ADP-ribosyl bond hydrolysis
Macro2-type e, v ADP-ribosyl bond hydrolysis
SUD-M-like v RNA binding
DUF2362 e unknown
a, Archaea; b, Bacteria; e, Eukarya; v, Virus


Structure

The 3D structure of the Macro domain describes a mixed alpha/beta fold of a mixed beta sheet sandwiched between four helices with the ligand-binding pocket lies within the fold.[11] Several Macro domain-only domains are shorter than the structure of AF1521 and lack either the first strand or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site.[6][11][16][17]

See also

References

  1. ↑ "Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going?". Microbiol. Mol. Biol. Rev. 70 (3): 789–829. September 2006. doi:10.1128/MMBR.00040-05. PMID 16959969. 
  2. ↑ "Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites". J. Mol. Biol. 385 (1): 212–25. January 2009. doi:10.1016/j.jmb.2008.10.045. PMID 18983849. 
  3. ↑ "Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins". Nature 451 (7174): 81–5. January 2008. doi:10.1038/nature06420. PMID 18172500. Bibcode: 2008Natur.451...81A. 
  4. ↑ "A biochemical genomics approach for identifying genes by the activity of their products". Science 286 (5442): 1153–5. November 1999. doi:10.1126/science.286.5442.1153. PMID 10550052. 
  5. ↑ Aravind L (May 2001). "The WWE domain: a common interaction module in protein ubiquitination and ADP ribosylation". Trends Biochem. Sci. 26 (5): 273–5. doi:10.1016/s0968-0004(01)01787-x. PMID 11343911. 
  6. ↑ 6.0 6.1 "The crystal structure of AF1521 a protein from Archaeoglobus fulgidus with homology to the non-histone domain of macroH2A". J. Mol. Biol. 330 (3): 503–11. July 2003. doi:10.1016/S0022-2836(03)00473-X. PMID 12842467. 
  7. ↑ "Chromatin regulation and genome maintenance by mammalian SIRT6". Trends in Biochemical Sciences 36 (1): 39–46. January 2011. doi:10.1016/j.tibs.2010.07.009. PMID 20729089. 
  8. ↑ "The roles of PARP1 in gene control and cell differentiation". Current Opinion in Genetics & Development 20 (5): 512–8. October 2010. doi:10.1016/j.gde.2010.06.001. PMID 20591646. 
  9. ↑ "The macro domain protein family: Structure, functions, and their potential therapeutic implications". Mutation Research 727 (3): 86–103. 2011. doi:10.1016/j.mrrev.2011.03.001. PMID 21421074. 
  10. ↑ "Poly(ADP-ribose): novel functions for an old molecule". Nature Reviews Molecular Cell Biology 7 (7): 517–28. July 2006. doi:10.1038/nrm1963. PMID 16829982. 
  11. ↑ 11.0 11.1 11.2 "The macro domain is an ADP-ribose binding module". EMBO J. 24 (11): 1911–20. June 2005. doi:10.1038/sj.emboj.7600664. PMID 15902274. 
  12. ↑ Takamura-Enya, Takeji; Watanabe, Masahiko; Totsuka, Yukari; Kanazawa, Takashi; Matsushima-Hibiya, Yuko; Koyama, Kotaro; Sugimura, Takashi; Wakabayashi, Keiji (2001-10-23). "Mono(ADP-ribosyl)ation of 2′-deoxyguanosine residue in DNA by an apoptosis-inducing protein, pierisin-1, from cabbage butterfly" (in en). Proceedings of the National Academy of Sciences 98 (22): 12414–12419. doi:10.1073/pnas.221444598. ISSN 0027-8424. PMID 11592983. Bibcode: 2001PNAS...9812414T. 
  13. ↑ Lyons, Bronwyn; Ravulapalli, Ravikiran; Lanoue, Jason; Lugo, Miguel R.; Dutta, Debajyoti; Carlin, Stephanie; Merrill, A. Rod (2016-05-20). "Scabin, a Novel DNA-acting ADP-ribosyltransferase from Streptomyces scabies". The Journal of Biological Chemistry 291 (21): 11198–11215. doi:10.1074/jbc.M115.707653. ISSN 1083-351X. PMID 27002155. 
  14. ↑ 14.0 14.1 Jankevicius, Gytis; Ariza, Antonio; Ahel, Marijan; Ahel, Ivan (2016). "The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA". Molecular Cell 64 (6): 1109–1116. doi:10.1016/j.molcel.2016.11.014. PMID 27939941. 
  15. ↑ 15.0 15.1 Schuller, Marion; Butler, Rachel E.; Ariza, Antonio; Tromans-Coia, Callum; Jankevicius, Gytis; Claridge, Tim D. W.; Kendall, Sharon L.; Goh, Shan et al. (2021-08-18). "Molecular basis for DarT ADP-ribosylation of a DNA base" (in en). Nature 596 (7873): 597–602. doi:10.1038/s41586-021-03825-4. ISSN 1476-4687. PMID 34408320. https://www.nature.com/articles/s41586-021-03825-4. 
  16. ↑ 16.0 16.1 "Splicing regulates NAD metabolite binding to histone macroH2A". Nat. Struct. Mol. Biol. 12 (7): 624–5. July 2005. doi:10.1038/nsmb956. PMID 15965484. 
  17. ↑ "Structural and functional basis for ADP-ribose and poly(ADP-ribose) binding by viral macro domains". J. Virol. 80 (17): 8493–502. September 2006. doi:10.1128/JVI.00713-06. PMID 16912299. 
This article incorporates text from the public domain Pfam and InterPro: IPR002589



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