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322  structures 6188  species 5  interactions 15094  sequences 172  architectures

Family: SIR2 (PF02146)

Summary: Sir2 family

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Sirtuin". More...

Sirtuin Edit Wikipedia article

Sir2 family
1SZD.png
Crystallographic structure of yeast sir2 (rainbow colored cartoon, N-terminus = blue, C-terminus = red) complexed with ADP (space-filling model, carbon = white, oxygen = red, nitrogen = blue, phosphorus = orange) and a histone H4 peptide (magenta) containing an acylated lysine residue (displayed as spheres).[1]
Identifiers
SymbolSIR2
PfamPF02146
Pfam clanCL0085
InterProIPR003000
PROSITEPS50305
SCOPe1j8f / SUPFAM

Sirtuins are a class of proteins that possess either mono-ADP-ribosyltransferase, or deacylase activity, including deacetylase, desuccinylase, demalonylase, demyristoylase and depalmitoylase activity.[2][3][4] The name Sir2 comes from the yeast gene 'silent mating-type information regulation 2',[5] the gene responsible for cellular regulation in yeast.

From in vitro studies, sirtuins are implicated in influencing cellular processes like aging, transcription, apoptosis, inflammation[6] and stress resistance, as well as energy efficiency and alertness during low-calorie situations.[7] As of 2018, there was no clinical evidence that sirtuins affect human aging.[8]

Yeast Sir2 and some, but not all, sirtuins are protein deacetylases. Unlike other known protein deacetylases, which simply hydrolyze acetyl-lysine residues, the sirtuin-mediated deacetylation reaction couples lysine deacetylation to NAD hydrolysis. This hydrolysis yields O-acetyl-ADP-ribose, the deacetylated substrate and nicotinamide, which is an inhibitor of sirtuin activity itself. The dependence of sirtuins on NAD links their enzymatic activity directly to the energy status of the cell via the cellular NAD:NADH ratio, the absolute levels of NAD, NADH or nicotinamide or a combination of these variables.

Sirtuins that deacetylate histones are structurally and mechanistically distinct from other classes of histone deacetylases (classes I, IIA, IIB and IV), which have a different protein fold and use Zn2+ as a cofactor.[9][10]

Actions and species distribution

Sirtuins are a family of signaling proteins involved in metabolic regulation.[11][12] They are ancient in animal evolution and appear to possess a highly conserved structure throughout all kingdoms of life.[11] Whereas bacteria and archaea encode either one or two sirtuins, eukaryotes encode several sirtuins in their genomes. In yeast, roundworms, and fruitflies, sir2 is the name of one of the sirtuin-type proteins (see table below).[13] Research on sirtuin protein started in 1991 by Leonard Guarente of MIT.[14][15] Mammals possess seven sirtuins (SIRT1–7) that occupy different subcellular compartments: SIRT1, SIRT6 and SIRT7 are predominantly in the nucleus, SIRT2 in the cytoplasm, and SIRT3, SIRT4 and SIRT5 in the mitochondria.[11]

Types

The first sirtuin was identified in yeast (a lower eukaryote) and named sir2. In more complex mammals, there are seven known enzymes that act in cellular regulation, as sir2 does in yeast. These genes are designated as belonging to different classes (I-IV), depending on their amino acid sequence structure.[16] Several gram positive prokaryotes as well as the gram negative hyperthermophilic bacterium Thermotoga maritima possess sirtuins that are intermediate in sequence between classes, and these are placed in the "undifferentiated" or "U" class. In addition, several Gram positive bacteria, including Staphylococcus aureus and Streptococcus pyogenes, as well as several fungi carry macrodomain-linked sirtuins (termed "class M" sirtuins).[4]

Class Subclass Species Intracellular
location
Activity Function
Bacteria Yeast Mouse Human
I a Sir2 or Sir2p,
Hst1 or Hst1p
Sirt1 SIRT1 nucleus, cytoplasm deacetylase metabolism
inflammation
b Hst2 or Hst2p Sirt2 SIRT2 nucleus and cytoplasm deacetylase cell cycle,
tumorigenesis
Sirt3 SIRT3 mitochondria deacetylase metabolism
c Hst3 or Hst3p,
Hst4 or Hst4p
II Sirt4 SIRT4 mitochondria ADP-ribosyl
transferase
insulin secretion
III Sirt5 SIRT5 mitochondria demalonylase, desuccinylase and deacetylase ammonia detoxification
IV a Sirt6 SIRT6 nucleus Demyristoylase, depalmitoylase, ADP-ribosyl
transferase and deacetylase
DNA repair,
metabolism,
TNF secretion
b Sirt7 SIRT7 nucleolus deacetylase rRNA
transcription
U cobB[17] regulation of
acetyl-CoA synthetase[18]
metabolism
M SirTM[4] ADP-ribosyl transferase ROS detoxification

SIRT3, a mitochondrial protein deacetylase, plays a role in the regulation of multiple metabolic proteins like isocitrate dehydrogenase of the TCA cycle. It also plays a role in skeletal muscle as a metabolic adaptive response. Since glutamine is a source of a-ketoglutarate used to replenish the TCA cycle, SIRT4 is involved in glutamine metabolism.[19]

Aging

Although preliminary studies with resveratrol, an activator of deacetylases such as SIRT1,[20] led some scientists to speculate that resveratrol may extend lifespan, there was no clinical evidence for such an effect, as of 2018.[8]

In vitro studies shown that calorie restriction regulates the plasma membrane redox system, involved in mitochondrial homeostasis, and the reduction of inflammation through cross-talks between SIRT1 and AMP-activated protein kinase (AMPK),[21][22][23] but the role of sirtuins in longevity is still unclear,[20][21][23] as calorie restriction in yeast could extend lifespan in the absence of Sir2 or other sirtuins, while the in vivo activation of Sir2 by calorie restriction or resveratrol to extend lifespan has been challenged in multiple organisms.[24]

Tissue fibrosis

A 2018 review indicated that SIRT levels are lower in tissues from people with scleroderma, and such reduced SIRT levels may increase risk of fibrosis through modulation of the TGF-β signaling pathway.[25]

DNA repair

SIRT1, SIRT6 and SIRT7 proteins are employed in DNA repair.[26] SIRT1 protein promotes homologous recombination in human cells and is involved in recombinational repair of DNA breaks.[27]

SIRT6 is a chromatin-associated protein and in mammalian cells is required for base excision repair of DNA damage.[28] SIRT6 deficiency in mice leads to a degenerative aging-like phenotype.[28] In addition, SIRT6 promotes the repair of DNA double-strand breaks.[29] Furthermore, over-expression of SIRT6 can stimulate homologous recombinational repair.[30]

SIRT7 knockout mice display features of premature aging.[31] SIRT7 protein is required for repair of double-strand breaks by non-homologous end joining.[31]

Inhibitors

Sirtuin activity is inhibited by nicotinamide, which binds to a specific receptor site.[32]

See also

References

  1. ^ PDB: 1szd​; Zhao K, Harshaw R, Chai X, Marmorstein R (June 2004). "Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD(+)-dependent Sir2 histone/protein deacetylases". Proceedings of the National Academy of Sciences of the United States of America. 101 (23): 8563–8. Bibcode:2004PNAS..101.8563Z. doi:10.1073/pnas.0401057101. PMC 423234. PMID 15150415.
  2. ^ Du J, Zhou Y, Su X, Yu JJ, Khan S, Jiang H, Kim J, Woo J, Kim JH, Choi BH, He B, Chen W, Zhang S, Cerione RA, Auwerx J, Hao Q, Lin H (November 2011). "Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase". Science. 334 (6057): 806–9. Bibcode:2011Sci...334..806D. doi:10.1126/science.1207861. PMC 3217313. PMID 22076378.
  3. ^ Jiang H, Khan S, Wang Y, Charron G, He B, Sebastian C, Du J, Kim R, Ge E, Mostoslavsky R, Hang HC, Hao Q, Lin H (April 2013). "SIRT6 regulates TNF-α secretion through hydrolysis of long-chain fatty acyl lysine". Nature. 496 (7443): 110–3. Bibcode:2013Natur.496..110J. doi:10.1038/nature12038. PMC 3635073. PMID 23552949.
  4. ^ a b c Rack JG, Morra R, Barkauskaite E, Kraehenbuehl R, Ariza A, Qu Y, Ortmayer M, Leidecker O, Cameron DR, Matic I, Peleg AY, Leys D, Traven A, Ahel I (July 2015). "Identification of a Class of Protein ADP-Ribosylating Sirtuins in Microbial Pathogens". Molecular Cell. 59 (2): 309–20. doi:10.1016/j.molcel.2015.06.013. PMC 4518038. PMID 26166706.
  5. ^ EntrezGene 23410
  6. ^ Preyat N, Leo O (May 2013). "Sirtuin deacylases: a molecular link between metabolism and immunity". Journal of Leukocyte Biology. 93 (5): 669–80. doi:10.1189/jlb.1112557. PMID 23325925.
  7. ^ Satoh A, Brace CS, Ben-Josef G, West T, Wozniak DF, Holtzman DM, Herzog ED, Imai S (July 2010). "SIRT1 promotes the central adaptive response to diet restriction through activation of the dorsomedial and lateral nuclei of the hypothalamus". The Journal of Neuroscience. 30 (30): 10220–32. doi:10.1523/JNEUROSCI.1385-10.2010. PMC 2922851. PMID 20668205.
  8. ^ a b Shetty, Ashok K.; Kodali, Maheedhar; Upadhya, Raghavendra; Madhu, Leelavathi N. (2018). "Emerging anti-aging strategies - scientific basis and efficacy (Review)". Aging and Disease. 9 (6): 1165–1184. doi:10.14336/ad.2018.1026. ISSN 2152-5250. PMC 6284760. PMID 30574426.
  9. ^ Bürger M, Chory J (2018). "Structural and chemical biology of deacetylases for carbohydrates, proteins, small molecules and histones". Communications Biology. 1: 217. doi:10.1038/s42003-018-0214-4. PMC 6281622. PMID 30534609.
  10. ^ Marks PA, Xu WS (July 2009). "Histone deacetylase inhibitors: Potential in cancer therapy". Journal of Cellular Biochemistry. 107 (4): 600–8. doi:10.1002/jcb.22185. PMC 2766855. PMID 19459166.
  11. ^ a b c Ye, X; Li, M; Hou, T; Gao, T; Zhu, WG; Yang, Y (3 January 2017). "Sirtuins in glucose and lipid metabolism". Oncotarget (Review). 8 (1): 1845–1859. doi:10.18632/oncotarget.12157. PMC 5352102. PMID 27659520.
  12. ^ Yamamoto H, Schoonjans K, Auwerx J (August 2007). "Sirtuin functions in health and disease". Molecular Endocrinology. 21 (8): 1745–55. doi:10.1210/me.2007-0079. PMID 17456799.
  13. ^ Blander G, Guarente L (2004). "The Sir2 family of protein deacetylases". Annual Review of Biochemistry. 73 (1): 417–35. doi:10.1146/annurev.biochem.73.011303.073651. PMID 15189148.
  14. ^ Wade N (2006-11-08). "The quest for a way around aging". Health & Science. International Herald Tribune. Retrieved 2008-11-30.
  15. ^ "MIT researchers uncover new information about anti-aging gene". Massachusetts Institute of Technology, News Office. 2000-02-16. Retrieved 2008-11-30.
  16. ^ Dryden SC, Nahhas FA, Nowak JE, Goustin AS, Tainsky MA (May 2003). "Role for human SIRT2 NAD-dependent deacetylase activity in control of mitotic exit in the cell cycle". Molecular and Cellular Biology. 23 (9): 3173–85. doi:10.1128/MCB.23.9.3173-3185.2003. PMC 153197. PMID 12697818.
  17. ^ Zhao K, Chai X, Marmorstein R (March 2004). "Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Escherichia coli". Journal of Molecular Biology. 337 (3): 731–41. doi:10.1016/j.jmb.2004.01.060. PMID 15019790.
  18. ^ Schwer B, Verdin E (February 2008). "Conserved metabolic regulatory functions of sirtuins". Cell Metabolism. 7 (2): 104–12. doi:10.1016/j.cmet.2007.11.006. PMID 18249170.
  19. ^ Choi JE, Mostoslavsky R (June 2014). "Sirtuins, metabolism, and DNA repair". Current Opinion in Genetics & Development. 26: 24–32. doi:10.1016/j.gde.2014.05.005. PMC 4254145. PMID 25005742.
  20. ^ a b Aunan, JR; Watson, MM; Hagland, HR; Søreide, K (January 2016). "Molecular and biological hallmarks of ageing". The British Journal of Surgery (Review (in vitro)). 103 (2): e29–46. doi:10.1002/bjs.10053. PMID 26771470.
  21. ^ a b López-Lluch, G; Navas, P (15 April 2016). "Calorie restriction as an intervention in ageing". The Journal of Physiology (Review). 594 (8): 2043–60. doi:10.1113/JP270543. PMC 4834802. PMID 26607973.
  22. ^ Wang, Y; Liang, Y; Vanhoutte, PM (6 April 2011). "SIRT1 and AMPK in regulating mammalian senescence: a critical review and a working model". FEBS Letters (Review). 585 (7): 986–94. doi:10.1016/j.febslet.2010.11.047. hdl:10722/142456. PMID 21130086.
  23. ^ a b Park, Seongjoon; Mori, Ryoichi; Shimokawa, Isao (8 May 2013). "Do sirtuins promote mammalian longevity?: A Critical review on its relevance to the longevity effect induced by calorie restriction". Molecules and Cells (Review). 35 (6): 474–480. doi:10.1007/s10059-013-0130-x. PMC 3887872. PMID 23661364.
  24. ^ Smith DL, Jr; Nagy, TR; Allison, DB (May 2010). "Calorie restriction: what recent results suggest for the future of ageing research". European Journal of Clinical Investigation (Review). 40 (5): 440–50. doi:10.1111/j.1365-2362.2010.02276.x. PMC 3073505. PMID 20534066.
  25. ^ Wyman AE, Atamas SP (March 2018). "Sirtuins and accelerated aging in scleroderma". Current Rheumatology Reports. 20 (4): 16. doi:10.1007/s11926-018-0724-6. PMC 5942182. PMID 29550994.
  26. ^ Vazquez BN, Thackray JK, Serrano L (March 2017). "Sirtuins and DNA damage repair: SIRT7 comes to play". Nucleus. 8 (2): 107–115. doi:10.1080/19491034.2016.1264552. PMC 5403131. PMID 28406750.
  27. ^ Uhl M, Csernok A, Aydin S, Kreienberg R, Wiesmüller L, Gatz SA (April 2010). "Role of SIRT1 in homologous recombination". DNA Repair. 9 (4): 383–93. doi:10.1016/j.dnarep.2009.12.020. PMID 20097625.
  28. ^ a b Mostoslavsky R, Chua KF, Lombard DB, Pang WW, Fischer MR, Gellon L, Liu P, Mostoslavsky G, Franco S, Murphy MM, Mills KD, Patel P, Hsu JT, Hong AL, Ford E, Cheng HL, Kennedy C, Nunez N, Bronson R, Frendewey D, Auerbach W, Valenzuela D, Karow M, Hottiger MO, Hursting S, Barrett JC, Guarente L, Mulligan R, Demple B, Yancopoulos GD, Alt FW (January 2006). "Genomic instability and aging-like phenotype in the absence of mammalian SIRT6". Cell. 124 (2): 315–29. doi:10.1016/j.cell.2005.11.044. PMID 16439206.
  29. ^ McCord RA, Michishita E, Hong T, Berber E, Boxer LD, Kusumoto R, Guan S, Shi X, Gozani O, Burlingame AL, Bohr VA, Chua KF (January 2009). "SIRT6 stabilizes DNA-dependent protein kinase at chromatin for DNA double-strand break repair". Aging. 1 (1): 109–21. doi:10.18632/aging.100011. PMC 2815768. PMID 20157594.
  30. ^ Mao Z, Tian X, Van Meter M, Ke Z, Gorbunova V, Seluanov A (July 2012). "Sirtuin 6 (SIRT6) rescues the decline of homologous recombination repair during replicative senescence". Proceedings of the National Academy of Sciences of the United States of America. 109 (29): 11800–5. Bibcode:2012PNAS..10911800M. doi:10.1073/pnas.1200583109. PMC 3406824. PMID 22753495.
  31. ^ a b Vazquez BN, Thackray JK, Simonet NG, Kane-Goldsmith N, Martinez-Redondo P, Nguyen T, Bunting S, Vaquero A, Tischfield JA, Serrano L (July 2016). "SIRT7 promotes genome integrity and modulates non-homologous end joining DNA repair". The EMBO Journal. 35 (14): 1488–503. doi:10.15252/embj.201593499. PMC 4884211. PMID 27225932.
  32. ^ Avalos JL, Bever KM, Wolberger C (March 2005). "Mechanism of sirtuin inhibition by nicotinamide: altering the NAD(+) cosubstrate specificity of a Sir2 enzyme". Molecular Cell. 17 (6): 855–68. doi:10.1016/j.molcel.2005.02.022. PMID 15780941.

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Sir2 family Provide feedback

This region is characteristic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organisation and DNA damage repair processes [1].i

Literature references

  1. North BJ, Verdin E; , Genome Biol 2004;5:224.: Sirtuins: Sir2-related NAD-dependent protein deacetylases. PUBMED:15128440 EPMC:15128440


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003000

The sirtuin (also known as Sir2) family is broadly conserved from bacteria to human. Yeast Sir2 (silent mating-type information regulation 2), the founding member, was first isolated as part of the SIR complex required for maintaining a modified chromatin structure at telomeres. Sir2 functions in transcriptional silencing, cell cycle progression, and chromosome stability [PUBMED:7498786]. Although most sirtuins in eukaryotic cells are located in the nucleus, others are cytoplasmic or mitochondrial.

This family is divided into five classes (I-IV and U) on the basis of a phylogenetic analysis of 60 sirtuins from a wide array of organisms [PUBMED:10873683]. Class I and class IV are further divided into three and two subgroups, respectively. The U-class sirtuins are found only in Gram-positive bacteria [PUBMED:10873683]. The S. cerevisiae genome encodes five sirtuins, Sir2 and four additional proteins termed 'homologues of sir two' (Hst1p-Hst4p) [PUBMED:7498786]. The human genome encodes seven sirtuins, with representatives from classes I-IV [PUBMED:10873683,PUBMED:15128440].

Sirtuins are responsible for a newly classified chemical reaction, NAD-dependent protein deacetylation. The final products of the reaction are the deacetylated peptide and an acetyl ADP-ribose [PUBMED:11747420]. In nuclear sirtuins this deacetylation reaction is mainly directed against histones acetylated lysines [PUBMED:11722841].

Sirtuins typically consist of two optional and highly variable N- and C- terminal domain (50-300 aa) and a conserved catalytic core domain (~250 aa). Mutagenesis experiments suggest that the N- and C-terminal regions help direct catalytic core domain to different targets [PUBMED:11722841, PUBMED:10381378].

The 3D-structure of an archaeal sirtuin in complex with NAD reveals that the protein consists of a large domain having a Rossmann fold and a small domain containing a three-stranded zinc ribbon motif. NAD is bound in a pocket between the two domains [PUBMED:11336676].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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Pfam Clan

This family is a member of clan FAD_DHS (CL0085), which has the following description:

The members of this family adopt a Rossmann fold, similar to CLAN:CL0063. However, the members of this family are distinguished in that the FAD/NAD cofactor is bound in the opposite direction. In this arrangement, the adenosine moiety is found bound at the second half of the fold. In addition, the conserved GxGxxG motif found in classical NADP binding Rossmann folds is absent. Finally, another distinguishing characteristic is the formation of an internal hydrogen bond in the FAD molecule [1].

The clan contains the following 10 members:

CO_dh DS DUF4917 ETF_alpha PNTB PPS_PS SIR2 SIR2_2 TPP_enzyme_M TPP_enzyme_M_2

Alignments

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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  Seed
(18)
Full
(15094)
Representative proteomes UniProt
(45075)
NCBI
(61724)
Meta
(901)
RP15
(2469)
RP35
(6867)
RP55
(12677)
RP75
(20393)
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  Seed
(18)
Full
(15094)
Representative proteomes UniProt
(45075)
NCBI
(61724)
Meta
(901)
RP15
(2469)
RP35
(6867)
RP55
(12677)
RP75
(20393)
Alignment:
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  Seed
(18)
Full
(15094)
Representative proteomes UniProt
(45075)
NCBI
(61724)
Meta
(901)
RP15
(2469)
RP35
(6867)
RP55
(12677)
RP75
(20393)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

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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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.

Curation View help on the curation process

Seed source: IPR003000
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mian N , Bateman A
Number in seed: 18
Number in full: 15094
Average length of the domain: 170.50 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 52.99 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.6 21.6
Noise cut-off 21.5 21.5
Model length: 179
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 5 interactions for this family. More...

DUF592 Histone DUF592 AMP-binding_C SIR2

Structures

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 SIR2 domain has been found. There are 322 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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