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70  structures 1436  species 0  interactions 19247  sequences 281  architectures

Family: TUDOR (PF00567)

Summary: Tudor domain

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Tudor domain Edit Wikipedia article

TUDOR domain
PDB 2diq EBI.jpg
Structure of a TUDOR domain.
Symbol TUDOR
Pfam PF00567
Pfam clan CL0049
InterPro IPR008191
SCOP 3fdr
CDD cd04508

In molecular biology a tudor domain is a conserved protein structural domain originally identified as a region of 50 amino acids found in the Tudor protein encoded in Drosophila. 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.[1]

The proteins TP53BP1 (Tumor suppressor p53-binding protein 1) and its fission yeast homolog Crb2[2] and JMJD2A (Jumonji domain containing 2A) contain either tandem or double Tudor domains and recognize methylated histones.[3][4]

Other tudor domain containing proteins include AKAP1 (A-kinase anchor protein 1)[5] 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.[6] SND1 is involved in RISC complex and interacts with AEG-1 oncogene.[7] SND1 is also acts as an oncogene and plays a very important role in HCC and colon cancer.[8] The SND1 tudor domain binds to methylated arginine in the PIWIL1 protein.[9] Tudor containing SND1 promotes tumor angiogenesis in human hepatocellular carcinoma through a novel pathway which involves NF-kappaB and miR-221.[10] Tudor SND1 is also present in the Drosophila melanogaster. [11]


  1. ^ 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". J. Mol. Biol. 327 (2): 507–20. PMID 12628254. doi:10.1016/S0022-2836(03)00148-7. 
  2. ^ Botuyan MV, Lee J, Ward IM, et al. (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. PMC 1804291Freely accessible. PMID 17190600. doi:10.1016/j.cell.2006.10.043. 
  3. ^ 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. PMID 16601153. doi:10.1126/science.1125162. 
  4. ^ 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". Nat. Struct. Mol. Biol. 15 (1): 109–11. PMC 2211384Freely accessible. PMID 18084306. doi:10.1038/nsmb1326. 
  5. ^ Rogne M, Landsverk HB, Van Eynde A, et al. (December 2006). "The KH-Tudor domain of a-kinase anchoring protein 149 mediates RNA-dependent self-association". Biochemistry. 45 (50): 14980–9. PMID 17154535. doi:10.1021/bi061418y. 
  6. ^ Caudy AA, Ketting RF, Hammond SM, Denli AM, Bathoorn AM, Tops BB, Silva JM, Myers MM, Hannon GJ, Plasterk RH (September 2003). "A micrococcal nuclease homologue in RNAi effector complexes". Nature. 425 (6956): 411–4. PMID 14508492. doi:10.1038/nature01956. 
  7. ^ Yoo BK, Santhekadur PK, Gredler R, Chen D, Emdad L, Bhutia S, Pannell L, Fisher PB, Sarkar D (2011). "Increased RNA-induced silencing complex (RISC) activity contributes to hepatocellular carcinoma". Hepatology. 53 (5): 1538–48. PMC 3081619Freely accessible. PMID 21520169. doi:10.1002/hep.24216. 
  8. ^ Yoo BK, Emdad L, Lee SG, Su ZZ, Santhekadur P, Chen D, Gredler R, Fisher PB, Sarkar D (April 2011). "Astrocyte elevated gene-1 (AEG-1): A multifunctional regulator of normal and abnormal physiology". Pharmacol. Ther. 130 (1): 1–8. PMC 3043119Freely accessible. PMID 21256156. doi:10.1016/j.pharmthera.2011.01.008. 
  9. ^ Liu K, Chen C, Guo Y, et al. (October 2010). "Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain". Proc. Natl. Acad. Sci. U.S.A. 107 (43): 18398–403. PMC 2972943Freely accessible. PMID 20937909. doi:10.1073/pnas.1013106107. 
  10. ^ Santhekadur PK, Das SK, Gredler R, 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". J. Biol. Chem. 287 (17): 13952–8. PMC 3340184Freely accessible. PMID 22396537. doi:10.1074/jbc.M111.321646. 
  11. ^ Muying Ying; Dahua Chen (2012). "Tudor domain-containing proteins of Drosophila melanogaster.". Development, Growth & Differentiation. 

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Literature references

  1. Ponting CP; , Trends Biochem Sci 1997;22:51-52.: Tudor domains in proteins that interact with RNA. PUBMED:9048482 EPMC:9048482

  2. Callebaut I, Mornon JP; , Biochem J 1997;321:125-132.: The human EBNA-2 coactivator p100: multidomain organization and relationship to the staphylococcal nuclease fold and to the tudor protein involved in Drosophila melanogaster development. PUBMED:9003410 EPMC:9003410

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002999

The drosophila Tudor protein, the founder of the Tudor domain family, is encoded by a 'posterior group' gene, which when mutated disrupt normal abdominal segmentation and pole cell formation. Another drosophila gene, homeless, is required for RNA localization during oogenesis. The tudor protein contains multiple repeats of a domain which is also found in homeless [ PUBMED:9048482 , PUBMED:23741747 ].

The tudor domain is found in many proteins that colocalise with ribonucleoprotein or single-strand DNA-associated complexes in the nucleus, in the mitochondrial membrane, or at kinetochores. At first it was not clear if the domain binds directly to RNA and ssDNA, or controls interactions with the nucleoprotein complexes but it is now known that this domain recognises and binds to methyl-arginine-lysine residues, playing important roles in diverse epigenetics, gene expression and the regulation of various small RNAs [ PUBMED:23741747 , PUBMED:21172665 , PUBMED:15955813 ]. The tudor-containing protein homeless, also contains a zinc finger typical of RNA-binding proteins [ PUBMED:9048482 ].

This domain has been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. One example is the Tudor domain of Survival of Motor Neuron (SMN), linked to spinal muscular atrophy, which binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The resolution of the solution structure of the Tudor domain of human SMN revealed that the Tudor domain forms a strongly bent antiparallel beta-sheet with five strands forming a barrel-like fold. The structure exhibits a conserved negatively charged surface that interacts with the C-terminal Arg and Gly-rich tails of the spliceosomal Sm D1 and D3 proteins [ PUBMED:11135666 , PUBMED:26700805 ].

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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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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...


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: Alignment kindly provided by SMART
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: SMART
Number in seed: 44
Number in full: 19247
Average length of the domain: 119.00 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 25.43 %

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 23.0 23.0
Trusted cut-off 23.0 23.0
Noise cut-off 22.9 22.9
Model length: 122
Family (HMM) version: 27
Download: download the raw HMM for this family

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 TUDOR domain has been found. There are 70 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
A0A0G2JWJ2 View 3D Structure Click here
A0A0G2K972 View 3D Structure Click here
A0A1D6H9E9 View 3D Structure Click here
A0A1D8PTZ1 View 3D Structure Click here
A0A2R8QE00 View 3D Structure Click here
A0A2R8QLW0 View 3D Structure Click here
A0A2R8QPQ1 View 3D Structure Click here
A0A2R8QQC4 View 3D Structure Click here
A1Z9P1 View 3D Structure Click here
A1ZAC4 View 3D Structure Click here
A4I7R1 View 3D Structure Click here
A6NAF9 View 3D Structure Click here
B4F7C4 View 3D Structure Click here
B5MCY1 View 3D Structure Click here
B8A4F4 View 3D Structure Click here
D3ZLP2 View 3D Structure Click here
D3ZXQ5 View 3D Structure Click here
D4A3N0 View 3D Structure Click here
E7FBS7 View 3D Structure Click here
E7FDW8 View 3D Structure Click here
F1LTR3 View 3D Structure Click here
F1R237 View 3D Structure Click here
F1R3C5 View 3D Structure Click here
F1RBY1 View 3D Structure Click here
G3V8T7 View 3D Structure Click here
I1JXS8 View 3D Structure Click here
I1K565 View 3D Structure Click here
I1KBV2 View 3D Structure Click here
I1KP14 View 3D Structure Click here
K7UVD7 View 3D Structure Click here
O08715 View 3D Structure Click here
O60522 View 3D Structure Click here
O88884 View 3D Structure Click here
P25823 View 3D Structure Click here
P34344 View 3D Structure Click here
P61407 View 3D Structure Click here
Q09285 View 3D Structure Click here
Q0E910 View 3D Structure Click here
Q14BI7 View 3D Structure Click here
Q19328 View 3D Structure Click here