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0  structures 292  species 0  interactions 461  sequences 64  architectures

Family: Apc5 (PF12862)

Summary: Anaphase-promoting complex subunit 5

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Anaphase-promoting complex subunit 5 Provide feedback

Apc5 is a subunit of the anaphase-promoting complex/cyclosome (APC/C) which is a multi-subunit ubiquitin ligase that mediates the proteolysis of cell cycle proteins in mitosis and G1. Apc5, although it does not harbour a classical RNA binding domain, Apc5 binds the poly(A) binding protein (PABP), which directly binds the internal ribosome entry site (IRES) of growth factor 2 mRNA. PABP was found to enhance IRES-mediated translation, whereas Apc5 over-expression counteracted this effect. In addition to its association with the APC/C complex, Apc5 binds much heavier complexes and co-sediments with the ribosomal fraction [1,2]. The N-terminus of Afi1 serves to stabilise the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC [3]. This region of the Apc5 member proteins carries a TPR-like motif.

Literature references

  1. Koloteva-Levine N, Pinchasi D, Pereman I, Zur A, Brandeis M, Elroy-Stein O;, Mol Cell Biol. 2004;24:3577-3587.: The Apc5 subunit of the anaphase-promoting complex/cyclosome interacts with poly(A) binding protein and represses internal ribosome entry site-mediated translation. PUBMED:15082755 EPMC:15082755

  2. Peters JM;, Nat Rev Mol Cell Biol. 2006;7:644-656.: The anaphase promoting complex/cyclosome: a machine designed to destroy. PUBMED:16896351 EPMC:16896351

  3. Ors A, Grimaldi M, Kimata Y, Wilkinson CR, Jones N, Yamano H;, J Biol Chem. 2009;284:23989-23994.: The transcription factor Atf1 binds and activates the APC/C ubiquitin ligase in fission yeast. PUBMED:19584054 EPMC:19584054


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR026000

This entry represents a domain of Apc5 that carries a TPR-like motif.

Apc5 is a subunit of the anaphase-promoting complex/cyclosome (APC/C) which is a multisubunit ubiquitin ligase that mediates the proteolysis of cell cycle proteins in mitosis and G1. Apc5, although it does not harbour a classical RNA binding domain, binds the poly(A) binding protein (PABP), which directly binds the internal ribosome entry site (IRES) of growth factor 2 mRNA. PABP was found to enhance IRES-mediated translation, whereas Apc5 over-expression counteracted this effect. In addition to its association with the APC/C complex, Apc5 binds much heavier complexes and co-sediments with the ribosomal fraction [PUBMED:15082755, PUBMED:16896351].

Domain organisation

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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
(26)
Full
(461)
Representative proteomes NCBI
(1604)
Meta
(191)
RP15
(95)
RP35
(155)
RP55
(224)
RP75
(278)
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Format an alignment

  Seed
(26)
Full
(461)
Representative proteomes NCBI
(1604)
Meta
(191)
RP15
(95)
RP35
(155)
RP55
(224)
RP75
(278)
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
(26)
Full
(461)
Representative proteomes NCBI
(1604)
Meta
(191)
RP15
(95)
RP35
(155)
RP55
(224)
RP75
(278)
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.

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.

Note: You can also download the data file for the tree.

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: JCSG
Previous IDs: none
Type: Domain
Author: Coggill P
Number in seed: 26
Number in full: 461
Average length of the domain: 89.20 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 16.11 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 3.9
Trusted cut-off 21.0 4.6
Noise cut-off 20.9 -1000000.0
Model length: 94
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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