Summary: Macro domain
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Macro domain Edit Wikipedia article
Crystal structure of the macro-domain of human core histone variant macroh2a1.1
|SCOPe||1vhu / SUPFAM|
In molecular biology, the Macro domain 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.
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. PMC 1594587. PMID 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. PMID 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. doi:10.1038/nature06420. PMID 18172500.
- 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. PMID 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. PMID 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. PMID 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. PMC 2991557. PMID 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. PMC 2942995. PMID 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. PMID 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. PMID 16829982.
- 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. PMC 1142602. PMID 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. doi:10.1073/pnas.221444598. ISSN 0027-8424. PMC 60068. PMID 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. ISSN 1083-351X. PMC 4900268. PMID 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. PMC 5179494. PMID 27939941.
- 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. PMID 15965484.
- 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. PMC 1563857. PMID 16912299.
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Macro domain Provide feedback
This domain is an ADP-ribose binding module. It is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein Q02874. This domain is found in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alphaviruses P03317. This domain is also found on its own in a family of proteins from bacteria P75918 archaebacteria O59182 and eukaryotes Q17432.
Martzen MR, McCraith SM, Spinelli SL, Torres FM, Fields S, Grayhack EJ, Phizicky EM; , Science 1999;286:1153-1155.: A biochemical genomics approach for identifying genes by the activity of their products. PUBMED:10550052 EPMC:10550052
Martzen MR, McCraith SM, Spinelli SL, Torres FM, Fields S, Grayhack EJ, Phizicky EM; , Science 1999;286:1153-1155.: A biochemical genomics approach for identifying genes by the activity of their products. PUBMED:10550052 EPMC:10550052
Internal database links
|Similarity to PfamA using HHSearch:||Macro_2|
External database links
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, 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 Macro domain has a mixed alpha/beta fold of a mixed beta sheet sandwiched between four helices. 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 [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:
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
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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 7 members:DUF2263 Macro Macro_2 PARG_cat Pdase_M17_N2 Peptidase_M17_N SUD-M
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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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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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
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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.
Note: You can also download the data file for the tree.
Curation and family details
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|
|Number in seed:||88|
|Number in full:||8832|
|Average length of the domain:||113.20 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||28.69 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||21|
|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.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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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.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
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.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
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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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 194 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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