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21  structures 1145  species 1  interaction 2595  sequences 53  architectures

Family: Autophagy_act_C (PF03987)

Summary: Autophagocytosis associated protein, active-site domain

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This is the Wikipedia entry entitled "Autophagocytosis associated protein Atg3". More...

Autophagocytosis associated protein Atg3 Edit Wikipedia article

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Autophagocytosis associated protein, active-site domain Provide feedback

Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex [2].

Literature references

  1. Schlumpberger M, Schaeffeler E, Straub M, Bredschneider M, Wolf DH, Thumm M; , J Bacteriol 1997;179:1068-1076.: AUT1, a gene essential for autophagocytosis in the yeast Saccharomyces cerevisiae. PUBMED:9023185 EPMC:9023185

  2. Mizushima N, Yoshimori T, Ohsumi Y; , FEBS Lett. 2002;532:450-454.: Mouse Apg10 as an Apg12-conjugating enzyme: analysis by the conjugation-mediated yeast two-hybrid method. PUBMED:12482611 EPMC:12482611

  3. Yamaguti M, Suzuki NN, Fujioka Y, Ohsumi Y, Inagaki F; , Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007;63:443-445.: Crystallization and preliminary X-ray analysis of Atg10. PUBMED:17565192 EPMC:17565192


This tab holds annotation information from the InterPro database.

InterPro entry IPR007135

Proteins in this entry belong to the Atg3 group of proteins and the Atg3 conjugation enzymes.

Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [PUBMED:11058089] and is induced by starvation [PUBMED:9190802]. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [PUBMED:11675007, PUBMED:18472412]. The breakdown of vesicular transport intermediates is a unique feature of autophagy [PUBMED:11058089]. Autophagy can also function in the elimination of invading bacteria and antigens [PUBMED:18472412].

Atg3 is the E2 enzyme for the LC3 lipidation process [PUBMED:18321988]. It is essential for autophagocytosis. The super protein complex, the Atg16L complex, consists of multiple Atg12-Atg5 conjugates. Atg16L has an E3-like role in the LC3 lipidation reaction. The activated intermediate, LC3-Atg3 (E2), is recruited to the site where the lipidation takes place [PUBMED:18398292].

Atg3 catalyses the conjugation of Atg8 and phosphatidylethanolamine (PE). Atg3 has an alpha/beta-fold, and its core region is topologically similar to canonical E2 enzymes. Atg3 has two regions inserted in the core region and another with a long alpha-helical structure that protrudes from the core region as far as 30 A [PUBMED:17227760]. It interacts with atg8 through an intermediate thioester bond between Cys-288 and the C-terminal Gly of atg8. It also interacts with the C-terminal region of the E1-like atg7 enzyme.

Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex [PUBMED:12482611].

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 TypeIII_Chap (CL0097), which has the following description:

The translocation of pathogenic proteins into a host cell is mediated by the type III secretory system. A component of this system is a chaperone, which binds to the protein which is going to be secreted in the bacterial cytosol and is involved in translocation of the secreted protein, although the chaperone is not translocated itself. An individual chaperone associates with one or two specific proteins [1]. There are a large number of type III secretory system chaperones, which are small acidic proteins and exhibit significant sequence divergence. This clan groups type III secretory system chaperones. Members with a known structure form small compact globular domains with an alpha-beta(3)- alpha-beta(2)-alpha like organisation [1].

The clan contains the following 6 members:

Autophagy_act_C CesT Chaperone_III DUF2299 Invas_SpaK YbjN

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 (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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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
(163)
Full
(2595)
Representative proteomes UniProt
(4240)
NCBI
(5099)
Meta
(9)
RP15
(440)
RP35
(1115)
RP55
(1800)
RP75
(2596)
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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
(163)
Full
(2595)
Representative proteomes UniProt
(4240)
NCBI
(5099)
Meta
(9)
RP15
(440)
RP35
(1115)
RP55
(1800)
RP75
(2596)
Alignment:
Format:
Order:
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
(163)
Full
(2595)
Representative proteomes UniProt
(4240)
NCBI
(5099)
Meta
(9)
RP15
(440)
RP35
(1115)
RP55
(1800)
RP75
(2596)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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_10019 (release 7.3)
Previous IDs: Autophagy_C;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Wood V , Coggill P
Number in seed: 163
Number in full: 2595
Average length of the domain: 231.90 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 80.83 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 206
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

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

ThiF

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 Autophagy_act_C domain has been found. There are 21 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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