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2  structures 252  species 0  interactions 968  sequences 23  architectures

Family: YTH (PF04146)

Summary: YT521-B-like domain

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This is the Wikipedia entry entitled "YTH protein domain". More...

YTH protein domain Edit Wikipedia article

YTH protein domain
Identifiers
Symbol YTH
Pfam PF04146
Pfam clan CL0178
InterPro IPR007275

In molecular biology, the protein domain, YTH refers to a member of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells.[1]

This protein domain, the YTH-domain, is conserved across all eukaryotes and suggests that the conserved C-terminal region plays a critical role in relaying the cytosolic Ca-signals to the nucleus, thereby regulating gene expression.[2]

Function/mechanism[edit]

It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B, SWISSPROT, is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner.[3] Additionally, it is also thought that YTH domain has a role in RNA binding. [4]

Structure[edit]

The domain is predicted to be a mixed alpha/beta-fold containing four alpha helices and six beta strands.[4]

Plant[edit]

In plant cells environmental stimuli, which light, pathogens, hormones, and abiotic stresses, elicit changes in the cytosolic calcium levels but little is known of the cytosolic-nuclear Ca-signaling pathway; where gene regulation occurs to respond appropriately to the stress. It has been demonstrated that two novel Arabidopsis thaliana (Mouse-ear cress) proteins, (ECT1 and ECT2), specifically associated with Calcineurin B-Like-Interacting Protein Kinase1 (CIPK1), a member of Ser/Thr protein kinases that interact with the calcineurin B-like Ca-binding proteins. These two proteins contain a very similar C-terminal region (180 amino acids in length, 81% similarity), which is required and sufficient for both interaction with CIPK1 and translocation to the nucleus.

References[edit]

  1. ^ Harigaya Y, Tanaka H, Yamanaka S, Tanaka K, Watanabe Y, Tsutsumi C, Chikashige Y, Hiraoka Y, Yamashita A, Yamamoto M (July 2006). "Selective elimination of messenger RNA prevents an incidence of untimely meiosis". Nature 442 (7098): 45–50. doi:10.1038/nature04881. PMID 16823445. 
  2. ^ Ok SH, Jeong HJ, Bae JM, Shin JS, Luan S, Kim KN (September 2005). "Novel CIPK1-associated proteins in Arabidopsis contain an evolutionarily conserved C-terminal region that mediates nuclear localization". Plant Physiol. 139 (1): 138–50. doi:10.1104/pp.105.065649. PMC 1203364. PMID 16113215. 
  3. ^ Hartmann AM, Nayler O, Schwaiger FW, Obermeier A, Stamm S (November 1999). "The interaction and colocalization of Sam68 with the splicing-associated factor YT521-B in nuclear dots is regulated by the Src family kinase p59(fyn)". Mol. Biol. Cell 10 (11): 3909–26. PMC 25688. PMID 10564280. 
  4. ^ a b Stoilov P, Rafalska I, Stamm S (October 2002). "YTH: a new domain in nuclear proteins". Trends Biochem. Sci. 27 (10): 495–7. doi:10.1016/S0968-0004(02)02189-8. PMID 12368078. 

This article incorporates text from the public domain Pfam and InterPro IPR007275

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.

YT521-B-like domain Provide feedback

A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells [3]. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein Q9QY02 YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner [1]. The YTH domain has been identified as part of the PUA superfamily [4].

Literature references

  1. Hartmann AM, Nayler O, Schwaiger FW, Obermeier A, Stamm S; , Mol Biol Cell 1999;10:3909-3926.: The interaction and colocalization of Sam68 with the splicing- associated factor YT521-B in nuclear dots is regulated by the Src family kinase p59fyn. PUBMED:10564280 EPMC:10564280

  2. Stoilov P, Rafalska I, Stamm S; , Trends Biochem Sci 2002;27:495-497.: YTH: a new domain in nuclear proteins. PUBMED:12368078 EPMC:12368078

  3. Harigaya Y, Tanaka H, Yamanaka S, Tanaka K, Watanabe Y, Tsutsumi C, Chikashige Y, Hiraoka Y, Yamashita A, Yamamoto M; , Nature. 2006;442:45-50.: Selective elimination of messenger RNA prevents an incidence of untimely meiosis. PUBMED:16823445 EPMC:16823445

  4. Bertonati C, Punta M, Fischer M, Yachdav G, Forouhar F, Zhou W, Kuzin AP, Seetharaman J, Abashidze M, Ramelot TA, Kennedy MA, Cort JR, Belachew A, Hunt JF, Tong L, Montelione GT, Rost B;, Proteins. 2009;75:760-773.: Structural genomics reveals EVE as a new ASCH/PUA-related domain. PUBMED:19191354 EPMC:19191354


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007275

A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells [PUBMED:16823445]. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanaisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B, SWISSPROT, is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner [PUBMED:10564280]. The domain is predicted to have four alpha helices and six beta strands [PUBMED:12368078].

In plant cells environmental stimuli, which light, pathogens, hormones, and abiotic stresses, elicit changes in the cytosolic Ca levels but little is known of the cytosolic-nuclear Ca-signaling pathway; where gene regulation occurs to respond appropriately to the stress. It has been demonstrated that two novel Arabidopsis thaliana (Mouse-ear cress) proteins, (ECT1 and ECT2), specifically associated with Calcineurin B-Like-Interacting Protein Kinase1 (CIPK1), a member of Ser/Thr protein kinases that interact with the calcineurin B-like Ca-binding proteins. These two proteins contain a very similar C-terminal region (180 amino acids in length, 81% similarity), which is required and sufficient for both interaction with CIPK1 and translocation to the nucleus. This domain, the YTH-domain, is conserved across all eukaryotes and suggests that the conserved C-terminal region plays a critical role in relaying the cytosolic Ca-signals to the nucleus, thereby regulating gene expression [PUBMED:16113215].

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 PUA (CL0178), which has the following description:

This clan consists of the RNA binding PUA domain and ASCH domain. It also contains uncharacterised protein families.

The clan contains the following 10 members:

ASCH DUF3850 EVE LON PUA PUA_2 TruB-C_2 TruB_C UPF0113 YTH

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(59)
Full
(968)
Representative proteomes NCBI
(870)
Meta
(5)
RP15
(150)
RP35
(268)
RP55
(403)
RP75
(553)
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Format an alignment

  Seed
(59)
Full
(968)
Representative proteomes NCBI
(870)
Meta
(5)
RP15
(150)
RP35
(268)
RP55
(403)
RP75
(553)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(59)
Full
(968)
Representative proteomes NCBI
(870)
Meta
(5)
RP15
(150)
RP35
(268)
RP55
(403)
RP75
(553)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

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:

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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: Pfam-B_1386 (release 7.3)
Previous IDs: YT521-B;
Type: Domain
Author: Bateman A
Number in seed: 59
Number in full: 968
Average length of the domain: 142.90 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 23.91 %

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 21.4 21.4
Trusted cut-off 21.4 23.3
Noise cut-off 20.9 21.3
Model length: 140
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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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 YTH 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 seqence.

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