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2  structures 246  species 1  interaction 282  sequences 8  architectures

Family: APG12 (PF04110)

Summary: Ubiquitin-like autophagy protein Apg12

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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.

Ubiquitin-like autophagy protein Apg12 Provide feedback

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells [1]. The Apg12 system is one of the ubiquitin-like protein conjugation systems conserved in eukaryotes. It was first discovered in yeast during systematic analyses of the apg mutants defective in autophagy. Covalent attachment of Apg12-Apg5 is essential for autophagy [2,3,4].

Literature references

  1. Suzuki K, Kirisako T, Kamada Y, Mizushima N, Noda T, Ohsumi Y; , EMBO J 2001;20:5971-5981.: The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. PUBMED:11689437 EPMC:11689437

  2. Kuma A, Mizushima N, Ishihara N, Ohsumi Y; , J Biol Chem 2002;277:18619-18625.: Formation of the approximately 350-kDa Apg12-Apg5.Apg16 multimeric complex, mediated by Apg16 oligomerization, is essential for autophagy in yeast. PUBMED:11897782 EPMC:11897782

  3. Mizushima N, Sugita H, Yoshimori T, Ohsumi Y; , J Biol Chem 1998;273:33889-33892.: A new protein conjugation system in human. The counterpart of the yeast Apg12p conjugation system essential for autophagy. PUBMED:9852036 EPMC:9852036

  4. Mizushima N, Yoshimori T, Ohsumi Y; , Int J Biochem Cell Biol 2003;35:553-561.: Role of the Apg12 conjugation system in mammalian autophagy. PUBMED:12672448 EPMC:12672448


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007242

Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole [PUBMED:11689437]. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate [PUBMED:10406794]. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway [PUBMED:10712513]. This entry represents Apg12, which is covalently bound to Apg5 [PUBMED:9852036].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 Ubiquitin (CL0072), which has the following description:

This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.

The clan contains the following 41 members:

APG12 Atg8 Blt1 Caps_synth_GfcC CIDE-N Cobl DUF1315 DUF2407 DUF4430 DWNN FERM_N Lambda_tail_I Multi_ubiq NQRA_SLBB PB1 PI3K_rbd Plug Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RBD SLBB Telomere_Sde2 TGS ThiS ThiS-like TmoB TUG-UBL1 Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 UBX Ufm1 UN_NPL4 Urm1 YchF-GTPase_C YukD

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
(6)
Full
(282)
Representative proteomes NCBI
(973)
Meta
(70)
RP15
(65)
RP35
(107)
RP55
(165)
RP75
(197)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(6)
Full
(282)
Representative proteomes NCBI
(973)
Meta
(70)
RP15
(65)
RP35
(107)
RP55
(165)
RP75
(197)
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
(6)
Full
(282)
Representative proteomes NCBI
(973)
Meta
(70)
RP15
(65)
RP35
(107)
RP55
(165)
RP75
(197)
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:

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: Pfam-B_9471 (release 7.3);
Previous IDs: none
Type: Family
Author: Wood V, Finn RD, Bateman A
Number in seed: 6
Number in full: 282
Average length of the domain: 83.60 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 53.46 %

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 20.9 20.9
Trusted cut-off 20.9 20.9
Noise cut-off 20.8 20.8
Model length: 87
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

APG12

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 APG12 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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