Summary: F-box domain
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F-box protein Edit Wikipedia article
| F-box linker domain | |||||||||
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Structure of the LRR linker domain of Skp2 in the Skp1-Skp2 complex.[1]
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| Identifiers | |||||||||
| Symbol | F-box | ||||||||
| Pfam | PF00646 | ||||||||
| Pfam clan | CL0271 | ||||||||
| InterPro | IPR001810 | ||||||||
| SMART | SM00256 | ||||||||
| PROSITE | PS50181 | ||||||||
| SCOP | 1fs2 | ||||||||
| SUPERFAMILY | 1fs2 | ||||||||
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F-box proteins are proteins containing at least one F-box domain. The first identified F-box protein is one of three components of the SCF complex, which mediates ubiquitination of proteins targeted for degradation by the 26S proteasome.
Core components
F-box domain is a protein structural motif of about 50 amino acids that mediates protein–protein interactions. It has consensus sequence and varies in few position. It was first identified in cyclin F.[2] The F-box motif of Skp2, consisting of three alpha-helices, interacts directly with the SCF protein Skp1.[3] F-box domains commonly exist in proteins in concert with other protein–protein interaction motifs such as leucine-rich repeats (illustrated in the Figure) and WD repeats, which are thought to mediate interactions with SCF substrates.[4]
Localization
The F-box protein is a big superfamily in Eukaryotic cells like yeast, plant, human. The F-box protein has been found on cytoplasm and nucleus. But it's hard to precisely decide which organism organ in cell does the F-box protein locate because the number of F-box protein is so much.[5]
Function
F-box proteins have also been associated with cellular functions such as signal transduction and regulation of the cell cycle.[6] In plants, many F-box proteins are represented in gene networks broadly regulated by microRNA-mediated gene silencing via RNA interference.[7] F-box proteins are involved in many plant vegetative and reproduction growth and development. For example, F-box protein-FOA1 involved in abscisic acid (ABA) signaling to affect the seed germination.[8] ACRE189/ACIF1 can regulate cell death and defense when the pathogen is recognized in the Tobacco and Tomato plant.[9]
In human cells, in high-iron condition, two iron atoms stabilise the F-Box FBXL5 and then the complex mediates the ubiquitination of IRP2.[10]
Regulation
F-box protein as a protein can be regulated in different mechanisms. The regulation can happen in the F-box protein synthesis process, protein degradation process and association with SCF complex process. For example, in yeast, the F-box protein Met30 can be ubiquitinated in a cullin-dependent manner.[11][11]
References
- ^ Schulman BA, Carrano AC, Jeffrey PD, et al. (November 2000). "Insights into SCF ubiquitin ligases from the structure of the Skp1-Skp2 complex". Nature. 408 (6810): 381–6. doi:10.1038/35042620. PMID 11099048.
- ^ Bai C, Sen P, Hofmann K, Ma L, Goebl M, Harper JW, Elledge SJ. "SKP1 connects cell cycle regulators to the ubiquitin proteolysis machinery through a novel motif, the F-box". Cell 86 263-74 1996.
- ^ Bai C, Sen P, Hofmann K, Ma L, Goebl M, Harper JW, Elledge SJ (July 1996). "SKP1 connects cell cycle regulators to the ubiquitin proteolysis machinery through a novel motif, the F-box". Cell. 86 (2): 263–74. doi:10.1016/S0092-8674(00)80098-7. PMID 8706131.
- ^ Kipreos ET, Pagano M (2000). "The F-box protein family". Genome Biol. 1 (5): REVIEWS3002. doi:10.1186/gb-2000-1-5-reviews3002. PMC 138887
. PMID 11178263. - ^ Rajasekharan, Sathyanath; Kennedy, Timothy E (2013). "Protein family review The netrin protein family".
- ^ Craig KL, Tyers M (1999). "The F-box: a new motif for ubiquitin dependent proteolysis in cell cycle regulation and signal transduction". Prog. Biophys. Mol. Biol. 72 (3): 299–328. doi:10.1016/S0079-6107(99)00010-3. PMID 10581972.
- ^ Jones-Rhoades MW, Bartel DP, Bartel B (2006). "MicroRNAS and their regulatory roles in plants". Annu Rev Plant Biol. 57: 19–53. doi:10.1146/annurev.arplant.57.032905.105218. PMID 16669754.
- ^ Peng, Juan; Yu, Dashi; Wang, Liqun; Xie, Minmin; Yuan, Congying; Wang, Yu; Tang, Dongying; Zhao, Xiaoying; Liu, Xuanming (June 2012). "Arabidopsis F-box gene FOA1 involved in ABA signaling". Science China. Life Sciences. 55 (6): 497–506. doi:10.1007/s11427-012-4332-9. ISSN 1869-1889. PMID 22744179.
- ^ Ha, Van Den Burg; Tsitsigiannis, D. I.; Rowland, O; Lo, J; Rallapalli, G; Maclean, D; Takken, F. L.; Jones, J. D. (2008). "The F-box protein ACRE189/ACIF1 regulates cell death and defense responses activated during pathogen recognition in tobacco and tomato". Plant Cell. 20 (3): 697.
- ^ Moroishi, T; Nishiyama, M; Takeda, Y; Iwai, K; Nakayama, K. I. (2011). "The FBXL5-IRP2 axis is integral to control of iron metabolism in vivo". Cell Metabolism. 14 (3): 339.
- ^ Kaiser, Peter; Su, Ning-Yuan; Yen, James L.; Ouni, Ikram; Flick, Karin (2006-08-08). "The yeast ubiquitin ligase SCFMet30: connecting environmental and intracellular conditions to cell division". Cell Division. 1: 16. doi:10.1186/1747-1028-1-16. ISSN 1747-1028.
Further reading
- Ho M, Tsai P, Chien C (2006). "F-box proteins: the key to protein degradation". J Biomed Sci. 13 (2): 181–91. doi:10.1007/s11373-005-9058-2. PMID 16463014.
External links
- F-Box Proteins at the US National Library of Medicine Medical Subject Headings (MeSH)
- F-box motifs at the US National Library of Medicine Medical Subject Headings (MeSH)
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.
F-box domain Provide feedback
This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; PF00560 and PF07723) and the WD repeat (PF00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression [3].
Literature references
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Bai C, Sen P, Hofmann K, Ma L, Goebl M, Harper JW, Elledge SJ; , Cell 1996;86:263-274.: SKP1 connects cell cycle regulators to the ubiquitin proteolysis machinery through a novel motif, the F-box. PUBMED:8706131 EPMC:8706131
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Skowyra D, Craig KL, Tyers M, Elledge SJ, Harper JW; , Cell. 1997;91:209-219.: F-box proteins are receptors that recruit phosphorylated substrates to the SCF ubiquitin-ligase complex. PUBMED:9346238 EPMC:9346238
Internal database links
| SCOOP: | Elongin_A F-box-like F-box_4 F-box_5 |
| Similarity to PfamA using HHSearch: | F-box-like F-box_4 F-box_5 |
External database links
| PROSITE profile: | PS50181 |
| SCOP: | 1fs2 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001810
First identified in cyclin-F as a protein-protein interaction motif, the F-box is a conserved domain that is present in numerous proteins with a bipartite structure [PUBMED:8706131]. Through the F-box, these proteins are linked to the Skp1 protein and the core of SCFs (Skp1-cullin-F-box protein ligase) complexes. SCFs complexes constitute a new class of E3 ligases [PUBMED:9346238]. They function in combination with the E2 enzyme Cdc34 to ubiquitinate G1 cyclins, Cdk inhibitors and many other proteins, to mark them for degradation. The binding of the specific substrates by SCFs complexes is mediated by divergent protein-protein interaction motifs present in F-box proteins, like WD40 repeats, leucine rich repeats [PUBMED:9529603, PUBMED:10581972] or ANK repeats.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Molecular function | protein binding (GO:0005515) |
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 F-box (CL0271), which has the following description:
This clan includes classical F-boxes and the PRANC domain found in pox ankyrin proteins.
The clan contains the following 7 members:
Elongin_A F-box F-box-like F-box-like_2 F-box_4 F-box_5 PRANCAlignments
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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| Seed (430) |
Full (38971) |
Representative proteomes | UniProt (50939) |
NCBI (110192) |
Meta (98) |
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| RP15 (7632) |
RP35 (22868) |
RP55 (33370) |
RP75 (38985) |
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| PP/heatmap | 1 | ||||||||
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| Seed (430) |
Full (38971) |
Representative proteomes | UniProt (50939) |
NCBI (110192) |
Meta (98) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (7632) |
RP35 (22868) |
RP55 (33370) |
RP75 (38985) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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...
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
| Seed source: | Prosite |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Bateman A 
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| Number in seed: | 430 |
| Number in full: | 38971 |
| Average length of the domain: | 45.10 aa |
| Average identity of full alignment: | 21 % |
| Average coverage of the sequence by the domain: | 10.15 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 48 | ||||||||||||
| Family (HMM) version: | 33 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
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Eukaryota
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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 F-box domain has been found. There are 11 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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