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111  structures 336  species 0  interactions 4702  sequences 61  architectures

Family: Tudor_2 (PF18104)

Summary: Jumonji domain-containing protein 2A Tudor domain

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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.
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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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.

Jumonji domain-containing protein 2A Tudor domain Provide feedback

This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms [3]. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD) [6].

Literature references

  1. Ballare C, Lange M, Lapinaite A, Martin GM, Morey L, Pascual G, Liefke R, Simon B, Shi Y, Gozani O, Carlomagno T, Benitah SA, Di Croce L;, Nat Struct Mol Biol. 2012;19:1257-1265.: Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. PUBMED:23104054 EPMC:23104054

  2. Huang Y, Fang J, Bedford MT, Zhang Y, Xu RM;, Science. 2006;312:748-751.: Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. PUBMED:16601153 EPMC:16601153

  3. Lee J, Thompson JR, Botuyan MV, Mer G;, Nat Struct Mol Biol. 2008;15:109-111.: Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor. PUBMED:18084306 EPMC:18084306

  4. Cai L, Rothbart SB, Lu R, Xu B, Chen WY, Tripathy A, Rockowitz S, Zheng D, Patel DJ, Allis CD, Strahl BD, Song J, Wang GG;, Mol Cell. 2013;49:571-582.: An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. PUBMED:23273982 EPMC:23273982

  5. Musselman CA, Avvakumov N, Watanabe R, Abraham CG, Lalonde ME, Hong Z, Allen C, Roy S, Nunez JK, Nickoloff J, Kulesza CA, Yasui A, Cote J, Kutateladze TG;, Nat Struct Mol Biol. 2012;19:1266-1272.: Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1. PUBMED:23142980 EPMC:23142980

  6. Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN Jr, Denu JM;, Nat Commun. 2016;7:13387.: Reader domain specificity and lysine demethylase-4 family function. PUBMED:27841353 EPMC:27841353

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR040477

This is the tudor domain found in lysine-specific demethylase 4A (KDM4A, also known as JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms [ PUBMED:18084306 ]. KDM4 belongs to the conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD) [ PUBMED:27841353 ].

Domain organisation

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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: ECOD:EUF00901
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: El-Gebali S
Number in seed: 51
Number in full: 4702
Average length of the domain: 35.10 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 5.91 %

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 31.4 31.4
Trusted cut-off 31.4 31.4
Noise cut-off 31.3 31.3
Model length: 35
Family (HMM) version: 4
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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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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_2 domain has been found. There are 111 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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