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2  structures 1596  species 0  interactions 2229  sequences 31  architectures

Family: Hva1_TUDOR (PF11160)

Summary: Hypervirulence associated proteins TUDOR domain

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 "Domain of unknown function". More...

Domain of unknown function Edit Wikipedia article

A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.[1]

The DUF designation is tentative, and such families tend to be renamed to a more specific name (or merged to an existing domain) after a function is identified.[2][3]


The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[4] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.[2]


Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved. This (2009) work showed that about two thirds of DUF families had a structure similar to a previously solved one and therefore likely to be divergent members of existing protein superfamilies, whereas about one third possessed a novel protein fold.[5]

Some DUF families share remote sequence homology with domains that has characterized function. Computational work can be used to link these relationships. A 2015 work was able to assign 20% of the DUFs to characterized structural superfamilies.[6] Pfam also continuously perform the (manually-verified) assignment in "clan" superfamily entries.[1]

Frequency and conservation

Protein domains and DUFs in different domains of life. Left: Annotated domains. Right: domains of unknown function. Not all overlaps shown.[7]

More than 20% of all protein domains were annotated as DUFs in 2013. About 2,700 DUFs are found in bacteria compared with just over 1,500 in eukaryotes. Over 800 DUFs are shared between bacteria and eukaryotes, and about 300 of these are also present in archaea. A total of 2,786 bacterial Pfam domains even occur in animals, including 320 DUFs.[7]

Role in biology

Many DUFs are highly conserved, indicating an important role in biology. However, many such DUFs are not essential, hence their biological role often remains unknown. For instance, DUF143 is present in most bacteria and eukaryotic genomes.[8] However, when it was deleted in Escherichia coli no obvious phenotype was detected. Later it was shown that the proteins that contain DUF143, are ribosomal silencing factors that block the assembly of the two ribosomal subunits.[8] While this function is not essential, it helps the cells to adapt to low nutrient conditions by shutting down protein biosynthesis. As a result, these proteins and the DUF only become relevant when the cells starve.[8] It is thus believed that many DUFs (or proteins of unknown function, PUFs) are only required under certain conditions.

Essential DUFs

Goodacre et al. identified 238 DUFs in 355 essential proteins (in 16 model bacterial species), most of which represent single-domain proteins, clearly establishing the biological essentiality of DUFs. These DUFs are called "essential DUFs" or eDUFs.[7]

External links


  1. ^ a b El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer EL, Hirsh L, Paladin L, Piovesan D, Tosatto SC, Finn RD (January 2019). "The Pfam protein families database in 2019". Nucleic Acids Research. 47 (D1): D427–D432. doi:10.1093/nar/gky995. PMC 6324024. PMID 30357350.
  2. ^ a b Bateman A, Coggill P, Finn RD (October 2010). "DUFs: families in search of function". Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 66 (Pt 10): 1148–52. doi:10.1107/S1744309110001685. PMC 2954198. PMID 20944204.
  3. ^ Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD (January 2012). "The Pfam protein families database". Nucleic Acids Research. 40 (Database issue): D290-301. doi:10.1093/nar/gkr1065. PMC 3245129. PMID 22127870.
  4. ^ Schultz J, Milpetz F, Bork P, Ponting CP (May 1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proceedings of the National Academy of Sciences of the United States of America. 95 (11): 5857–64. Bibcode:1998PNAS...95.5857S. doi:10.1073/pnas.95.11.5857. PMC 34487. PMID 9600884.
  5. ^ Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, Wilson IA, Godzik A (September 2009). "Exploration of uncharted regions of the protein universe". PLOS Biology. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874. PMID 19787035.
  6. ^ Mudgal R, Sandhya S, Chandra N, Srinivasan N (July 2015). "De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods". Biology Direct. 10 (1): 38. doi:10.1186/s13062-015-0069-2. PMC 4520260. PMID 26228684.
  7. ^ a b c Goodacre NF, Gerloff DL, Uetz P (December 2013). "Protein domains of unknown function are essential in bacteria". mBio. 5 (1): e00744-13. doi:10.1128/mBio.00744-13. PMC 3884060. PMID 24381303.
  8. ^ a b c Häuser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N, Stellberger T, Diefenbacher ME, Nierhaus KH, Uetz P (2012). Hughes D (ed.). "RsfA (YbeB) proteins are conserved ribosomal silencing factors". PLOS Genetics. 8 (7): e1002815. doi:10.1371/journal.pgen.1002815. PMC 3400551. PMID 22829778.

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

This is the Wikipedia entry entitled "Tudor domain". More...

Tudor domain Edit Wikipedia article

TUDOR domain
PDB 2diq EBI.jpg
Structure of a TUDOR domain.
Pfam clanCL0049

In molecular biology, a Tudor domain is a conserved protein structural domain originally identified in the Tudor protein encoded in Drosophila.[1] The Tudor gene was found in a Drosophila screen for maternal factors that regulate embryonic development or fertility.[2] Mutations here are lethal for offspring, inspiring the name Tudor, as a reference to the Tudor King Henry VIII and the several miscarriages experienced by his wives.[1]


A Tudor domain is a protein region approximately 60 amino acids in length, which folds into an SH3-like structure with a five-stranded antiparallel beta-barrel form.[1] Tudor domains can further be organized into functional units consisting of either a single Tudor domain, tandem Tudor domains, or hybrid Tudor domains consisting of two Tudor domains linked by an anti-parallel beta-sheet made from their shared second and third beta-strands.[1] An essential component of the Tudor domain structure is the aromatic-binding cage formed by several (typically 4–5) aromatic amino acid residues.[1]

Interaction with methylated residues

Tudor domains exert their functions by recognizing and binding methylated lysine and arginine residues, allowing them to function as histone readers in an epigenetic context.[1] This occurs through cation–pi interactions between the methylated Arg/Lys residue and the aromatic residues of the Tudor domain's aromatic-binding cage.[1] Depending on the Tudor domain, this interaction can be methylation state-specific (mono-, di-, or trimethylation).[1]


DNA transcription and modification

Tudor domain proteins are involved in epigenetic regulation and can alter transcription by recognizing post-translational histone modifications and as adaptor proteins.[2] Recognition of methylated arginine and lysine histone residues results in the recruitment of downstream effectors, leading to chromatin silencing or activation depending on the Tudor domain protein and context.[1] For example, the human TDRD3 protein binds methylated arginine residues and promotes transcription of estrogen-responsive elements.[3] Conversely, the Polycomb-like protein (PCL) acts as an adaptor to recruit components of the Polycomb repressive complex 2 (PRC2), a histone H3K27 methyltransferase that represses transcription.[4] Additionally, Tudor domain proteins can repress transcription by recruiting DNA-methyltransferases to promote DNA methylation and heterochromatin assembly.[1] Tudor domain proteins also have the function of maintaining and propagating epigenetic modifications.[1]

Genome stability

The Tudor domain is involved in the silencing of selfish genetic elements, such as retrotransposons.[5] This functionality is performed both directly through Tudor-containing proteins, such as Tdrd7, as well as through piRNA synthesis.[6] Tudor domains are essential in the localization of protein machinery involved in piRNA creation, such as localization of Yb protein to the Yb body, assembly of the pole plasm in Drosophila, and recruitment of proteins to load Piwi with piRNA.[5]

DNA damage response

The human p53-binding protein 1 (TRP53BP1) is a Tudor domain protein involved in the DNA damage response (DDR) pathway, which functions to protect the genome from external stimuli.[5] It is a cascade of events that senses damage through adaptor proteins and triggers responses including cell cycle arrest, DNA repair, transcriptional modifications, and apoptosis.[5] TRP53BP1s Tudor domain mediates binding to sensors that accumulate at the sites of damage, and also functions as the adaptor promoting effector recruitment to the damaged sites.[5] TRP53BP1 is essential for DDR as it plays a very complex role in the regulation and recruitment of multiple other proteins involved.[5]

RNA metabolism

Tudor domain proteins involved in RNA metabolism have an extended Tudor domain of approximately 180 amino acids.[5] These proteins contain RNA-binding motifs to target RNAs, or bind to dimethylated arginines of proteins bound to RNAs.[5] These proteins regulate multiple aspects of RNA metabolism, including processing, stability, translation, and small RNA pathways.[5] Specifically, the survival motor neuron (SMN) protein is a Tudor domain protein that mediates the assembly of snRNPs (small nuclear ribonucleoproteins), by binding snRNAs and recruiting asymmetrically dimethylated arginines of SM proteins that form the protein constituent of snRNPs.[5] SMN promotes the maturation of snRNPs, which are essential for spliceosome assembly and intron removal.[5]


Hybrid Tudor domain in JMJD2A[7]

The proteins TP53BP1 (Tumor suppressor p53-binding protein 1) and its fission yeast homolog Crb2[8] and JMJD2A (Jumonji domain containing 2A) contain either tandem or double Tudor domains and recognize methylated histones.[9][10]

The structurally characterized Tudor domain in human SMN (survival of motor neuron) is a strongly bent anti-parallel β-sheet consisting of five β-strands with a barrel-like fold and recognizes symmetrically dimethylated arginine.[11]

Other Tudor domain containing proteins include AKAP1 (A-kinase anchor protein 1)[12] and ARID4A (AT rich interactive domain 4A) among others. A well known Tudor domain containing protein is Staphylococcal Nuclease Domain Containing 1 (SND1)/Tudor-SN/p100 co activator.[13] SND1 is involved in RISC complex and interacts with AEG-1 oncogene.[14] SND1 is also acts as an oncogene and plays a very important role in HCC and colon cancer.[15] The SND1 Tudor domain binds to methylated arginine in the PIWIL1 protein.[16] Tudor containing SND1 promotes tumor angiogenesis in human hepatocellular carcinoma through a novel pathway which involves NF-kappaB and miR-221.[17] Tudor SND1 is also present in the Drosophila melanogaster.[6]


  1. ^ a b c d e f g h i j k Botuyan MV, Mer G (2016). "Tudor Domains as Methyl-Lysine and Methyl-Arginine Readers". Chromatin Signaling and Diseases. Elsevier. pp. 149–165. doi:10.1016/b978-0-12-802389-1.00008-3. ISBN 978-0-12-802389-1.
  2. ^ a b Lu R, Wang GG (November 2013). "Tudor: a versatile family of histone methylation 'readers'". Trends in Biochemical Sciences. 38 (11): 546–55. doi:10.1016/j.tibs.2013.08.002. PMC 3830939. PMID 24035451.
  3. ^ Yang Y, Lu Y, Espejo A, Wu J, Xu W, Liang S, Bedford MT (December 2010). "TDRD3 is an effector molecule for arginine-methylated histone marks". Molecular Cell. 40 (6): 1016–23. doi:10.1016/j.molcel.2010.11.024. PMC 3090733. PMID 21172665.
  4. ^ Cai L, Rothbart SB, Lu R, Xu B, Chen WY, Tripathy A, et al. (February 2013). "An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting". Molecular Cell. 49 (3): 571–82. doi:10.1016/j.molcel.2012.11.026. PMC 3570589. PMID 23273982.
  5. ^ a b c d e f g h i j k Pek JW, Anand A, Kai T (July 2012). "Tudor domain proteins in development". Development. 139 (13): 2255–66. doi:10.1242/dev.073304. PMID 22669818. S2CID 26275277.
  6. ^ a b Ying M, Chen D (January 2012). "Tudor domain-containing proteins of Drosophila melanogaster". Development, Growth & Differentiation. 54 (1): 32–43. doi:10.1111/j.1440-169x.2011.01308.x. PMID 23741747. S2CID 23227910.
  7. ^ Ozboyaci M, Gursoy A, Erman B, Keskin O (March 2011). "Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study". PLOS ONE. 6 (3): e14765. Bibcode:2011PLoSO...614765O. doi:10.1371/journal.pone.0014765. PMC 3064570. PMID 21464980.
  8. ^ Botuyan MV, Lee J, Ward IM, Kim JE, Thompson JR, Chen J, Mer G (December 2006). "Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair". Cell. 127 (7): 1361–73. doi:10.1016/j.cell.2006.10.043. PMC 1804291. PMID 17190600.
  9. ^ Huang Y, Fang J, Bedford MT, Zhang Y, Xu RM (May 2006). "Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A". Science. 312 (5774): 748–51. Bibcode:2006Sci...312..748H. doi:10.1126/science.1125162. PMID 16601153. S2CID 20036710.
  10. ^ Lee J, Thompson JR, Botuyan MV, Mer G (January 2008). "Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor". Nature Structural & Molecular Biology. 15 (1): 109–11. doi:10.1038/nsmb1326. PMC 2211384. PMID 18084306.
  11. ^ Sprangers R, Groves MR, Sinning I, Sattler M (March 2003). "High-resolution X-ray and NMR structures of the SMN Tudor domain: conformational variation in the binding site for symmetrically dimethylated arginine residues". Journal of Molecular Biology. 327 (2): 507–20. doi:10.1016/s0022-2836(03)00148-7. PMID 12628254.
  12. ^ Rogne M, Landsverk HB, Van Eynde A, Beullens M, Bollen M, Collas P, Küntziger T (December 2006). "The KH-Tudor domain of a-kinase anchoring protein 149 mediates RNA-dependent self-association". Biochemistry. 45 (50): 14980–9. doi:10.1021/bi061418y. PMID 17154535.
  13. ^ Caudy AA, Ketting RF, Hammond SM, Denli AM, Bathoorn AM, Tops BB, et al. (September 2003). "A micrococcal nuclease homologue in RNAi effector complexes". Nature. 425 (6956): 411–4. Bibcode:2003Natur.425..411C. doi:10.1038/nature01956. PMID 14508492. S2CID 4410688.
  14. ^ Yoo BK, Santhekadur PK, Gredler R, Chen D, Emdad L, Bhutia S, et al. (May 2011). "Increased RNA-induced silencing complex (RISC) activity contributes to hepatocellular carcinoma". Hepatology. 53 (5): 1538–48. doi:10.1002/hep.24216. PMC 3081619. PMID 21520169.
  15. ^ Yoo BK, Emdad L, Lee SG, Su ZZ, Santhekadur P, Chen D, et al. (April 2011). "Astrocyte elevated gene-1 (AEG-1): A multifunctional regulator of normal and abnormal physiology". Pharmacology & Therapeutics. 130 (1): 1–8. doi:10.1016/j.pharmthera.2011.01.008. PMC 3043119. PMID 21256156.
  16. ^ Liu K, Chen C, Guo Y, Lam R, Bian C, Xu C, et al. (October 2010). "Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain". Proceedings of the National Academy of Sciences of the United States of America. 107 (43): 18398–403. Bibcode:2010PNAS..10718398L. doi:10.1073/pnas.1013106107. PMC 2972943. PMID 20937909.
  17. ^ Santhekadur PK, Das SK, Gredler R, Chen D, Srivastava J, Robertson C, et al. (April 2012). "Multifunction protein staphylococcal nuclease domain containing 1 (SND1) promotes tumor angiogenesis in human hepatocellular carcinoma through novel pathway that involves nuclear factor κB and miR-221". The Journal of Biological Chemistry. 287 (17): 13952–8. doi:10.1074/jbc.M111.321646. PMC 3340184. PMID 22396537.

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.

Hypervirulence associated proteins TUDOR domain Provide feedback

Family members include HVA1 (hypervirulence-associated protein 1) whose absence is associated with a hypervirulent phenotype in mice. Metabolomics analysis suggests that when HVA1 is absent there is a block in the citric acid cycle, while structural analysis of the Hva1 protein suggests a potential interaction with NADPH. The structural architecture of Hva1 bears similarity with Tudor domains [1].

Literature references

  1. McClelland EE, Ramagopal UA, Rivera J, Cox J, Nakouzi A, Prabu MM, Almo SC, Casadevall A;, PLoS Pathog. 2016;12:e1005849.: A Small Protein Associated with Fungal Energy Metabolism Affects the Virulence of Cryptococcus neoformans in Mammals. PUBMED:27583447 EPMC:27583447

This tab holds annotation information from the InterPro database.

InterPro entry IPR021331

Proteins containing this domain include HVA1 (hypervirulence-associated protein 1) whose absence is associated with a hypervirulent phenotype in mice. Metabolomics analysis suggests that when HVA1 is absent there is a block in the citric acid cycle, while structural analysis of the Hva1 protein suggests a potential interaction with NADPH. The structural architecture of Hva1 bears similarity with Tudor domains [ PUBMED:27583447 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Tudor (CL0049), which has the following description:

This clan covers the Tudor domain 'royal family' [1]. This includes chromo, MBT, PWWP and tudor domains. The chromo domain is a comprised of approximately 50 amino acid residues. There are usually one to three Chromo domains found in a single protein. In some chromo domain containing proteins, a second related chromo domain has been found and is referred to as the Chromo-shadow domain. The structure of the Chromo and Chromo-shadow domains reveal an OB-fold, a fold found in a variety of prokaryotic and eukaryotic nucleic acid binding proteins. More specifically,the chromo-domain structure reveals a three beta strands that are packed against an alpha helix. Interestingly, a similar structure is found in the archaeal chromatin proteins (7kDa DNA-binding domain). These are sequence neutral DNA binding proteins. The DNA binding in these archaeal proteins is mediated through the triple stranded beta sheet. These archaeal domains are though to represent an ancestral chromo domain. Homologs of the chromo domain have been found in fission yeast, ciliated protozoa and all animal species, but appear to be absent in eubacteria, budding yeast and plants [2]. The precise function of the chromo domain is unclear, but the chromo domain is thought to act as a targeting module for chromosomal proteins, although the chromosomal contexts and functional contexts being targeted vary. In all cases studies, the chromo domains are found in proteins that are involved in transcription regulation, positive and negative [2].

The clan contains the following 33 members:

53-BP1_Tudor 7kD_DNA_binding Agenet Chromo Chromo_2 Chromo_shadow Cul7 DUF1325 DUF4537 DUF4819 GEN1_C Hva1_TUDOR LBR_tudor LytTR MBT Mtf2_C ProQ_C PWWP Rad9_Rad53_bind RBB1NT SAWADEE SMN SNase TTD TUDOR Tudor-knot Tudor_1_RapA Tudor_2 Tudor_3 Tudor_4 Tudor_5 Tudor_FRX1 Tudor_RapA


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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_002448 (release 23.0)
Previous IDs: DUF2945;
Type: Domain
Sequence Ontology: SO:0000417
Author: Pollington J , Finn RD , El-Gebali S
Number in seed: 177
Number in full: 2229
Average length of the domain: 59.90 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 54.43 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.1 24.1
Trusted cut-off 24.2 24.5
Noise cut-off 23.9 23.9
Model length: 59
Family (HMM) version: 11
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Species distribution

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Colour assignments

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


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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 Hva1_TUDOR domain has been found. There are 2 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.

Protein Predicted structure External Information
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