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0  structures 670  species 0  interactions 2128  sequences 3  architectures

Family: TCP (PF03634)

Summary: TCP family transcription factor

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

TCP protein domain Edit Wikipedia article

TCP
Identifiers
Symbol TCP
Pfam PF03634
InterPro IPR005333
PROSITE PDOC00610
SCOP 1grl
SUPERFAMILY 1grl

In molecular biology, the protein domain TCP is actually a family of transcription factors named after: teosinte branched 1 (tb1, Zea mays (Maize)),[1] cycloidea (cyc) (Antirrhinum majus) (Garden snapdragon)[2] and PCF in rice (Oryza sativa).[3][4]

Function[edit]

Members of the TCP protein domain family appear to be involved in cell proliferation. It may also have a role in signalling pathways since it has three phosphorylation sites. The TCP domain is necessary for specific binding to promoter elements of the Proliferating cell nuclear antigen (PCNA) gene and also in DNA binding.[2]

Evolution[edit]

This family of transcription factors are exclusive to higher plants. They can be divided into two groups, TCP-C and TCP-P, that appear to have separated following an early gene duplication event.[5] This duplication event may have led to functional divergence and it has been proposed that that the TCP-P subfamily are transcriptional repressors, while the TPC-C subfamily are transcription activators.[6]

Structure[edit]

The TCP proteins code for structurally related proteins implicated in the evolution of key morphological traits.[2] However, the biochemical function of CYC and TB1 proteins remains to be demonstrated. One of the conserved regions is predicted to form a non-canonical basic-Helix-Loop-Helix (bHLH) structure. This domain is also found in two rice DNA-binding proteins, PCF1 and PCF2, where it has been shown to be involved in DNA-binding and dimerization.

References[edit]

  1. ^ Finlayson SA (May 2007). "Arabidopsis Teosinte Branched1-like 1 regulates axillary bud outgrowth and is homologous to monocot Teosinte Branched1". Plant Cell Physiol. 48 (5): 667–77. doi:10.1093/pcp/pcm044. PMID 17452340. 
  2. ^ a b c Cubas P, Lauter N, Doebley J, Coen E (April 1999). "The TCP domain: a motif found in proteins regulating plant growth and development". Plant J. 18 (2): 215–22. PMID 10363373. 
  3. ^ Kosugi S, Ohashi Y (May 2002). "DNA binding and dimerization specificity and potential targets for the TCP protein family". Plant J. 30 (3): 337–48. PMID 12000681. 
  4. ^ Daele J, Mélon J (1979). "Skin tests, IgE and rast, nasal provocation test". Acta Otorhinolaryngol Belg 33 (4): 572–81. PMID 539398. 
  5. ^ Navaud O, Dabos P, Carnus E, Tremousaygue D, Hervé C (July 2007). "TCP transcription factors predate the emergence of land plants". J. Mol. Evol. 65 (1): 23–33. doi:10.1007/s00239-006-0174-z. PMID 17568984. 
  6. ^ Li C, Potuschak T, Colón-Carmona A, Gutiérrez RA, Doerner P (September 2005). "Arabidopsis TCP20 links regulation of growth and cell division control pathways". Proc. Natl. Acad. Sci. U.S.A. 102 (36): 12978–83. doi:10.1073/pnas.0504039102. PMC 1200278. PMID 16123132. 

This article incorporates text from the public domain Pfam and InterPro IPR005333

External links[edit]

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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.

TCP family transcription factor Provide feedback

This is a family of TCP plant transcription factors. TCP proteins were named after the first characterised members (TB1, CYC and PCFs) and they are involved in multiple developmental control pathways [1]. This region contains a DNA binding basic-Helix-Loop-Helix (bHLP) structure [1].

Literature references

  1. Cubas P, Lauter N, Doebley J, Coen E; , Plant J 1999;18:215-222.: The TCP domain: a motif found in proteins regulating plant growth and development. PUBMED:10363373 EPMC:10363373

  2. Koyama T, Furutani M, Tasaka M, Ohme-Takagi M; , Plant Cell. 2007;19:473-484.: TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis. PUBMED:17307931 EPMC:17307931

  3. Navaud O, Dabos P, Carnus E, Tremousaygue D, Herve C; , J Mol Evol. 2007;65:23-33.: TCP Transcription Factors Predate the Emergence of Land Plants. PUBMED:17568984 EPMC:17568984


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005333

The TCP transcription factor family was named after: teosinte branched 1 (tb1, Zea mays (Maize)) [PUBMED:17452340], cycloidea (cyc) (Antirrhinum majus) (Garden snapdragon) [PUBMED:10363373] and PCF in rice (Oryza sativa) [PUBMED:12000681, PUBMED:539398]. The TCP proteins code for structurally related proteins implicated in the evolution of key morphological traits [PUBMED:10363373]. However, the biochemical function of CYC and TB1 proteins remains to be demonstrated. One of the conserved regions is predicted to form a non-canonical basic-Helix-Loop-Helix (bHLP) structure. This domain is also found in two rice DNA-binding proteins, PCF1 and PCF2, where it has been shown to be involved in DNA-binding and dimerization.

This family of transcription factors are exclusive to higher plants. They can be divided into two groups, TCP-C and TCP-P, that appear to have separated following an early gene duplication event [PUBMED:17568984]. This duplication event may have led to functional divergence and it has been proposed that that the TCP-P subfamily are transcriptional repressors, while the TPC-C subfamily are transcription activators [PUBMED:16123132].

Domain organisation

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Alignments

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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
(113)
Full
(2128)
Representative proteomes NCBI
(2132)
Meta
(1)
RP15
(30)
RP35
(170)
RP55
(231)
RP75
(282)
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Format an alignment

  Seed
(113)
Full
(2128)
Representative proteomes NCBI
(2132)
Meta
(1)
RP15
(30)
RP35
(170)
RP55
(231)
RP75
(282)
Alignment:
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Sequence:
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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
(113)
Full
(2128)
Representative proteomes NCBI
(2132)
Meta
(1)
RP15
(30)
RP35
(170)
RP55
(231)
RP75
(282)
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

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Seed source: Pfam-B_1979 (release 7.0)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 113
Number in full: 2128
Average length of the domain: 128.50 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 54.94 %

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 19.9 17.0
Trusted cut-off 20.2 20.2
Noise cut-off 19.6 16.8
Model length: 138
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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