Macro domain

Last updated
Macro
PDB 1zr3 EBI.jpg
Crystal structure of the macro-domain of human core histone variant macroh2a1.1
Identifiers
SymbolMacro
Pfam PF01661
Pfam clan CL0223
InterPro IPR002589
SCOP2 1vhu / SCOPe / SUPFAM
CDD cd02749
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary

In molecular biology, the Macro domain (often also written macrodomain) or A1pp domain is an ancient, evolutionary conserved structural module found in all kingdoms of life as well as some viruses. [1] Macro domains are modules of about 180 amino acids that can bind ADP-ribose, an NAD metabolite, or related ligands. Binding to ADP-ribose can be either covalent or non-covalent: [2] in certain cases it is believed to bind non-covalently, [3] 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. [4]

Contents

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. [5] However, the domain has been renamed Macro as it is the C-terminal domain of mammalian core histone macro-H2A. [6] [7] 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. Zinc-containing macro domains (Zn-Macros) are primarily encountered in pathogenic microorganisms and have structurally distinct features from other macro domains, which include their function being strictly dependent on a catalytic zinc within the active site. [8] [9]

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, [10] cell differentiation and proliferation, [11] necrosis and apoptosis, [12] and long-term memory formation. [13] 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. [14]

ADP-ribosylation of DNA is relatively uncommon and has only been described for a small number of toxins that include pierisin, [15] scabin [16] and DarT. [17] [18] 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. [17] [18] The Macro domain from human, macroH2A1.1, binds an NAD metabolite O-acetyl-ADP-ribose. [19]

ClassSubclassSpeciesActivity
MacroH2A-likeeADP-ribose binding
MacroD-type'classic'a, b, e, vADP-ribosyl bond hydrolysis
Zn-dependentb, eADP-ribosyl bond hydrolysis
GDAP2-likeeADP-ribose binding
ALC1-likeb, eADP-ribose binding or ADP-ribosyl bond hydrolysis
PARG-likePARG_cateADP-ribosyl bond hydrolysis
mPARG (DUF2263)b, e, vADP-ribosyl bond hydrolysis
Macro2-typee, vADP-ribosyl bond hydrolysis
SUD-M-likevRNA binding
DUF2362eunknown
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. [14] 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. [7] [14] [19] [20]

See also

References

  1. ↑ Rack, Johannes Gregor Matthias; Perina, Dragutin; Ahel, Ivan (2016-06-02). "Macrodomains: Structure, Function, Evolution, and Catalytic Activities". Annual Review of Biochemistry. 85 (1): 431–454. doi:10.1146/annurev-biochem-060815-014935. ISSN   0066-4154. PMID   26844395.
  2. ↑ Hassa PO, Haenni SS, Elser M, Hottiger MO (September 2006). "Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going?". Microbiol. Mol. Biol. Rev. 70 (3): 789–829. doi:10.1128/MMBR.00040-05. PMC   1594587 . PMID   16959969.
  3. ↑ Neuvonen M, Ahola T (January 2009). "Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites". J. Mol. Biol. 385 (1): 212–25. doi:10.1016/j.jmb.2008.10.045. PMC   7094737 . PMID   18983849.
  4. ↑ Ahel I, Ahel D, Matsusaka T, Clark AJ, Pines J, Boulton SJ, West SC (January 2008). "Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins". Nature. 451 (7174): 81–5. Bibcode:2008Natur.451...81A. doi:10.1038/nature06420. PMID   18172500. S2CID   4417693.
  5. ↑ Martzen MR, McCraith SM, Spinelli SL, Torres FM, Fields S, Grayhack EJ, Phizicky EM (November 1999). "A biochemical genomics approach for identifying genes by the activity of their products". Science. 286 (5442): 1153–5. doi:10.1126/science.286.5442.1153. PMID   10550052.
  6. ↑ 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.
  7. 1 2 Allen MD, Buckle AM, Cordell SC, Löwe J, Bycroft M (July 2003). "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. doi:10.1016/S0022-2836(03)00473-X. PMID   12842467.
  8. ↑ Rack, Johannes Gregor Matthias; Morra, Rosa; Barkauskaite, Eva; Kraehenbuehl, Rolf; Ariza, Antonio; Qu, Yue; Ortmayer, Mary; Leidecker, Orsolya; Cameron, David R.; Matic, Ivan; Peleg, Anton Y.; Leys, David; Traven, Ana; Ahel, Ivan (July 2015). "Identification of a Class of Protein ADP-Ribosylating Sirtuins in Microbial Pathogens". Molecular Cell. 59 (2): 309–320. doi:10.1016/j.molcel.2015.06.013. PMC   4518038 . PMID   26166706.
  9. ↑ Ariza, Antonio; Liu, Qiang; Cowieson, Nathan; Ahel, Ivan; Filippov, Dmitri V.; Rack, Johannes Gregor Matthias (September 2024). "Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains". Journal of Biological Chemistry 107770. doi: 10.1016/j.jbc.2024.107770 . PMC   11490716 . PMID   39270823.
  10. ↑ Tennen RI, Chua KF (January 2011). "Chromatin regulation and genome maintenance by mammalian SIRT6". Trends in Biochemical Sciences . 36 (1): 39–46. doi:10.1016/j.tibs.2010.07.009. PMC   2991557 . PMID   20729089.
  11. ↑ Ji Y, Tulin AV (October 2010). "The roles of PARP1 in gene control and cell differentiation". Current Opinion in Genetics & Development . 20 (5): 512–8. doi:10.1016/j.gde.2010.06.001. PMC   2942995 . PMID   20591646.
  12. ↑ Han W, Li X, Fu X (2011). "The macro domain protein family: Structure, functions, and their potential therapeutic implications". Mutation Research . 727 (3): 86–103. Bibcode:2011MRRMR.727...86H. doi:10.1016/j.mrrev.2011.03.001. PMC   7110529 . PMID   21421074.
  13. ↑ Schreiber V, Dantzer F, Ame JC, de Murcia G (July 2006). "Poly(ADP-ribose): novel functions for an old molecule". Nature Reviews Molecular Cell Biology . 7 (7): 517–28. doi:10.1038/nrm1963. PMID   16829982. S2CID   22030625.
  14. 1 2 3 Karras GI, Kustatscher G, Buhecha HR, Allen MD, Pugieux C, Sait F, Bycroft M, Ladurner AG (June 2005). "The macro domain is an ADP-ribose binding module". EMBO J. 24 (11): 1911–20. doi:10.1038/sj.emboj.7600664. PMC   1142602 . PMID   15902274.
  15. ↑ 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". Proceedings of the National Academy of Sciences. 98 (22): 12414–12419. Bibcode:2001PNAS...9812414T. doi: 10.1073/pnas.221444598 . ISSN   0027-8424. PMC   60068 . PMID   11592983.
  16. ↑ 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. PMC   4900268 . PMID   27002155.
  17. 1 2 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. PMC   5179494 . PMID   27939941.
  18. 1 2 Schuller, Marion; Butler, Rachel E.; Ariza, Antonio; Tromans-Coia, Callum; Jankevicius, Gytis; Claridge, Tim D. W.; Kendall, Sharon L.; Goh, Shan; Stewart, Graham R.; Ahel, Ivan (2021-08-18). "Molecular basis for DarT ADP-ribosylation of a DNA base" . Nature. 596 (7873): 597–602. Bibcode:2021Natur.596..597S. doi:10.1038/s41586-021-03825-4. hdl: 2299/25013 . ISSN   1476-4687. PMID   34408320. S2CID   237214909.
  19. 1 2 Kustatscher G, Hothorn M, Pugieux C, Scheffzek K, Ladurner AG (July 2005). "Splicing regulates NAD metabolite binding to histone macroH2A". Nat. Struct. Mol. Biol. 12 (7): 624–5. doi:10.1038/nsmb956. PMID   15965484. S2CID   29456363.
  20. ↑ Egloff MP, Malet H, Putics A, Heinonen M, Dutartre H, Frangeul A, Gruez A, Campanacci V, Cambillau C, Ziebuhr J, Ahola T, Canard B (September 2006). "Structural and functional basis for ADP-ribose and poly(ADP-ribose) binding by viral macro domains". J. Virol. 80 (17): 8493–502. doi:10.1128/JVI.00713-06. PMC   1563857 . PMID   16912299.
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