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31  structures 277  species 2  interactions 3295  sequences 92  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.
Identifiers
Symbol TUDOR
Pfam PF00567
Pfam clan CL0049
InterPro IPR008191
SMART TUDOR
PROSITE PDOC50304
SCOP 3fdr
SUPERFAMILY 3fdr
CDD cd04508

In molecular biology a tudor domain is a conserved protein structural motif 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 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]

References[edit]

  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. doi:10.1016/S0022-2836(03)00148-7. PMID 12628254. 
  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. doi:10.1016/j.cell.2006.10.043. PMC 1804291. PMID 17190600. 
  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. doi:10.1126/science.1125162. PMID 16601153. 
  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. doi:10.1038/nsmb1326. PMC 2211384. PMID 18084306. 
  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. doi:10.1021/bi061418y. PMID 17154535. 
  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. doi:10.1038/nature01956. PMID 14508492. 
  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. doi:10.1002/hep.24216. PMC 3081619. PMID 21520169. 
  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. doi:10.1016/j.pharmthera.2011.01.008. PMC 3043119. PMID 21256156. 
  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. doi:10.1073/pnas.1013106107. PMC 2972943. PMID 20937909. 
  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. doi:10.1074/jbc.M111.321646. PMID 22396537. 
  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 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].

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. It is not known whether the domain binds directly to RNA and ssDNA, or controls interactions with the nucleoprotein complexes. At least one tudor-containing protein, homeless, also contains a zinc finger typical of RNA-binding proteins [PUBMED:9048482].

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].

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 14 members:

53-BP1_Tudor 7kD_DNA_binding Agenet Chromo Chromo_shadow DUF1325 DUF4537 MBT PWWP Rad9_Rad53_bind RBB1NT SMN TUDOR Tudor-knot

Alignments

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(6)
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  Seed
(48)
Full
(3295)
Representative proteomes NCBI
(3372)
Meta
(6)
RP15
(629)
RP35
(828)
RP55
(1457)
RP75
(2089)
Alignment:
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  Seed
(48)
Full
(3295)
Representative proteomes NCBI
(3372)
Meta
(6)
RP15
(629)
RP35
(828)
RP55
(1457)
RP75
(2089)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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: Alignment kindly provided by SMART
Previous IDs: none
Type: Domain
Author: SMART
Number in seed: 48
Number in full: 3295
Average length of the domain: 118.30 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 26.42 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.3
Model length: 122
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

TUDOR SNase

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 TUDOR domain has been found. There are 31 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 seqence.

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