Summary: Macro domain
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Macro domain Edit Wikipedia article
|SCOP2||1vhu / SCOPe / SUPFAM|
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: in certain cases it is believed to bind non-covalently, 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.
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. However, the domain has been renamed Macro as it is the C-terminal domain of mammalian core histone macro-H2A. 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, cell differentiation and proliferation, necrosis and apoptosis, and long-term memory formation. 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. ADP-ribosylation of DNA is relatively uncommon and has only been described for a small number of toxins that include pierisin, scabin and DarT. 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. The Macro domain from human, macroH2A1.1, binds an NAD metabolite O-acetyl-ADP-ribose.
|MacroD-type||â€˜classicâ€™||a, b, e, v||ADP-ribosyl bond hydrolysis|
|Zn-dependent||b, e||ADP-ribosyl bond hydrolysis|
|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|
|a, Archaea; b, Bacteria; e, Eukarya; v, Virus|
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. 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.
- 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): 789â€“829. doi:10.1128/MMBR.00040-05. PMCÂ 1594587. PMIDÂ 16959969.
- 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): 212â€“25. doi:10.1016/j.jmb.2008.10.045. PMCÂ 7094737. PMIDÂ 18983849.
- 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): 81â€“5. Bibcode:2008Natur.451...81A. doi:10.1038/nature06420. PMIDÂ 18172500. S2CIDÂ 4417693.
- 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): 1153â€“5. doi:10.1126/science.286.5442.1153. PMIDÂ 10550052.
- Aravind L (May 2001). "The WWE domain: a common interaction module in protein ubiquitination and ADP ribosylation". Trends Biochem. Sci. 26 (5): 273â€“5. doi:10.1016/s0968-0004(01)01787-x. PMIDÂ 11343911.
- Allen MD, Buckle AM, Cordell SC, LÃ¶we 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): 503â€“11. doi:10.1016/S0022-2836(03)00473-X. PMIDÂ 12842467.
- Tennen RI, Chua KF (January 2011). "Chromatin regulation and genome maintenance by mammalian SIRT6". Trends in Biochemical Sciences. 36 (1): 39â€“46. doi:10.1016/j.tibs.2010.07.009. PMCÂ 2991557. PMIDÂ 20729089.
- Ji Y, Tulin AV (October 2010). "The roles of PARP1 in gene control and cell differentiation". Current Opinion in Genetics & Development. 20 (5): 512â€“8. doi:10.1016/j.gde.2010.06.001. PMCÂ 2942995. PMIDÂ 20591646.
- Han W, Li X, Fu X (2011). "The macro domain protein family: Structure, functions, and their potential therapeutic implications". Mutation Research. 727 (3): 86â€“103. doi:10.1016/j.mrrev.2011.03.001. PMCÂ 7110529. PMIDÂ 21421074.
- 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): 517â€“28. doi:10.1038/nrm1963. PMIDÂ 16829982. S2CIDÂ 22030625.
- 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): 1911â€“20. doi:10.1038/sj.emboj.7600664. PMCÂ 1142602. PMIDÂ 15902274.
- 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 2â€²-deoxyguanosine residue in DNA by an apoptosis-inducing protein, pierisin-1, from cabbage butterfly". Proceedings of the National Academy of Sciences. 98 (22): 12414â€“12419. Bibcode:2001PNAS...9812414T. doi:10.1073/pnas.221444598. ISSNÂ 0027-8424. PMCÂ 60068. PMIDÂ 11592983.
- 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): 11198â€“11215. doi:10.1074/jbc.M115.707653. ISSNÂ 1083-351X. PMCÂ 4900268. PMIDÂ 27002155.
- Jankevicius, Gytis; Ariza, Antonio; Ahel, Marijan; Ahel, Ivan (2016). "The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA". Molecular Cell. 64 (6): 1109â€“1116. doi:10.1016/j.molcel.2016.11.014. PMCÂ 5179494. PMIDÂ 27939941.
- 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): 597â€“602. doi:10.1038/s41586-021-03825-4. ISSNÂ 1476-4687. PMIDÂ 34408320.
- 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): 624â€“5. doi:10.1038/nsmb956. PMIDÂ 15965484. S2CIDÂ 29456363.
- 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): 8493â€“502. doi:10.1128/JVI.00713-06. PMCÂ 1563857. PMIDÂ 16912299.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Macro domain Provide feedback
The Macro 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 could be either covalent or non-covalent  in certain cases it is believed to bind non-covalently ; 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 . This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein . The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site .
Hassa PO, Haenni SS, Elser M, Hottiger MO;, Microbiol Mol Biol Rev. 2006;70:789-829.: Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going?. PUBMED:16959969 EPMC:16959969
Ahel I, Ahel D, Matsusaka T, Clark AJ, Pines J, Boulton SJ, West SC;, Nature. 2008;451:81-85.: Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins. PUBMED:18172500 EPMC:18172500
Egloff MP, Malet H, Putics A, Heinonen M, Dutartre H, Frangeul A, Gruez A, Campanacci V, Cambillau C, Ziebuhr J, Ahola T, Canard B;, J Virol. 2006;80:8493-8502.: Structural and functional basis for ADP-ribose and poly(ADP-ribose) binding by viral macro domains. PUBMED:16912299 EPMC:16912299
Allen MD, Buckle AM, Cordell SC, Lowe J, Bycroft M;, J Mol Biol. 2003;330:503-511.: The crystal structure of AF1521 a protein from Archaeoglobus fulgidus with homology to the non-histone domain of macroH2A. PUBMED:12842467 EPMC:12842467
Internal database links
|Similarity to PfamA using HHSearch:||Macro_2|
This tab holds annotation information from the InterPro database.
InterPro entry IPR002589
The Macro 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 could be either covalent or non-covalent [ PUBMED:16959969 ]: in certain cases it is believed to bind non-covalently [ PUBMED:18983849 ]; 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 [ PUBMED:18172500 ]. The domain was described originally in association with ADP-ribose 1''-phosphate (Appr-1''-P) processing activity (A1pp) of the yeast YBR022W protein [ PUBMED:10550052 ]. The domain is also called Macro domain as it is the C-terminal domain of mammalian core histone macro-H2A [ PUBMED:11343911 , PUBMED:12842467 ]. Macro domain proteins can be found in eukaryotes, in (mostly pathogenic) bacteria, in archaea and in ssRNA viruses, such as coronaviruses [ PUBMED:21525212 , PUBMED:31095648 ], Rubella and Hepatitis E viruses. In vertebrates the domain occurs e.g. in histone macroH2A, in predicted poly-ADP-ribose polymerases (PARPs) and in B aggressive lymphoma (BAL) protein. The macro domain can be associated with catalytic domains, such as PARP, or sirtuin. The Macro domain can recognise ADP-ribose or in some cases poly-ADP-ribose, which can be involved in ADP-ribosylation reactions that occur in important processes, such as chromatin biology, DNA repair and transcription regulation [ PUBMED:15902274 ]. The human macroH2A1.1 Macro domain binds an NAD metabolite O-acetyl-ADP-ribose [ PUBMED:15965484 ]. The Macro domain has been suggested to play a regulatory role in ADP-ribosylation, which is involved in inter- and intracellular signaling, transcriptional regulation, DNA repair pathways and maintenance of genomic stability, telomere dynamics, cell differentiation and proliferation, and necrosis and apoptosis.
The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein [ PUBMED:16912299 ]. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site [ PUBMED:12842467 , PUBMED:15902274 , PUBMED:15965484 , PUBMED:16912299 ].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
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Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
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This superfamily includes the Macro domain as well as the amino terminal domain from peptidase M17 proteins.
The clan contains the following 8 members:bCoV_SUD_M DUF2263 DUF2362 Macro Macro_2 PARG_cat Pdase_M17_N2 Peptidase_M17_N
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Seed source:||Pfam-B_434 (release 4.1)|
|Author:||Bateman A , Mistry J , Wood V , Williams LS|
|Number in seed:||85|
|Number in full:||14562|
|Average length of the domain:||112.70 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||26.77 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||24|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
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If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Macro domain has been found. There are 829 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.