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14  structures 1005  species 2  interactions 1187  sequences 27  architectures

Family: Autophagy_N (PF03986)

Summary: Autophagocytosis associated protein (Atg3), N-terminal domain

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

Autophagocytosis associated protein Atg3 Edit Wikipedia article

Autophagocytosis associated protein N-terminal
Identifiers
Symbol Autophagy_N
Pfam PF03986
InterPro IPR007134
Autophagocytosis associated protein active site domain
Identifiers
Symbol Autophagy_act_C
Pfam PF03987
InterPro IPR007135
Autophagocytosis associated protein C-terminal
Identifiers
Symbol Autophagy_Cterm
Pfam PF10381
InterPro IPR019461

In molecular biology, autophagocytosis associated protein Atg3 is the E2 enzyme for the LC3 lipidation process.[1] 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.[2]

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.[3] 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 lysosome/vacuole. Atg3 is a ubiquitin like modifier that is topologically similar to the canonical E2 enzyme.[4] It catalyses the conjugation of Atg8 and phosphatidylethanolamine.[5]

Atg3 consists of three domains, an N-terminal domain, a catalytic domain and a C-terminal domain. The catalytic domain contains a cysteine residue within an HPC motif, this is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex.[6] The small C-terminal domain is likely to be a distinct binding region for the stability of the autophagosome complex.[7] It carries a highly characteristic conserved FLKF sequence motif.

References

  1. ^ Fujita N, Itoh T, Omori H, Fukuda M, Noda T, Yoshimori T (May 2008). "The Atg16L complex specifies the site of LC3 lipidation for membrane biogenesis in autophagy". Mol. Biol. Cell. 19 (5): 2092–100. doi:10.1091/mbc.E07-12-1257. PMC 2366860Freely accessible. PMID 18321988. 
  2. ^ Noda T, Fujita N, Yoshimori T (May 2008). "The Ubi brothers reunited". Autophagy. 4 (4): 540–1. doi:10.4161/auto.5973. PMID 18398292. 
  3. ^ Yamada Y, Suzuki NN, Hanada T, Ichimura Y, Kumeta H, Fujioka Y, Ohsumi Y, Inagaki F (March 2007). "The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation". J. Biol. Chem. 282 (11): 8036–43. doi:10.1074/jbc.M611473200. PMID 17227760. 
  4. ^ Tanida I, Tanida-Miyake E, Komatsu M, Ueno T, Kominami E (April 2002). "Human Apg3p/Aut1p homologue is an authentic E2 enzyme for multiple substrates, GATE-16, GABARAP, and MAP-LC3, and facilitates the conjugation of hApg12p to hApg5p". J. Biol. Chem. 277 (16): 13739–44. doi:10.1074/jbc.M200385200. PMID 11825910. 
  5. ^ Schlumpberger M, Schaeffeler E, Straub M, Bredschneider M, Wolf DH, Thumm M (February 1997). "AUT1, a gene essential for autophagocytosis in the yeast Saccharomyces cerevisiae". J. Bacteriol. 179 (4): 1068–76. PMC 178799Freely accessible. PMID 9023185. 
  6. ^ Mizushima N, Yoshimori T, Ohsumi Y (December 2002). "Mouse Apg10 as an Apg12-conjugating enzyme: analysis by the conjugation-mediated yeast two-hybrid method". FEBS Lett. 532 (3): 450–4. doi:10.1016/S0014-5793(02)03739-0. PMID 12482611. 
  7. ^ Mizushima N, Yoshimori T, Ohsumi Y (May 2003). "Role of the Apg12 conjugation system in mammalian autophagy". Int. J. Biochem. Cell Biol. 35 (5): 553–61. doi:10.1016/S1357-2725(02)00343-6. PMID 12672448. 

This article incorporates text from the public domain Pfam and InterPro IPR007134

This article incorporates text from the public domain Pfam and InterPro IPR007135

This article incorporates text from the public domain Pfam and InterPro IPR019461

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.

Autophagocytosis associated protein (Atg3), N-terminal domain Provide feedback

Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the lysosome/vacuole. Atg3 is a ubiquitin like modifier that is topologically similar to the canonical E2 enzyme [3]. It catalyses the conjugation of Atg8 and phosphatidylethanolamine [4].

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. Tanida I, Tanida-Miyake E, Komatsu M, Ueno T, Kominami E; , J Biol Chem. 2002;277:13739-13744.: Human Apg3p/Aut1p homologue is an authentic E2 enzyme for multiple substrates, GATE-16, GABARAP, and MAP-LC3, and facilitates the conjugation of hApg12p to hApg5p. PUBMED:11825910 EPMC:11825910

  3. Yamada Y, Suzuki NN, Hanada T, Ichimura Y, Kumeta H, Fujioka Y, Ohsumi Y, Inagaki F; , J Biol Chem. 2007;282:8036-8043.: The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation. PUBMED:17227760 EPMC:17227760

  4. Ichimura Y, Kirisako T, Takao T, Satomi Y, Shimonishi Y, Ishihara N, Mizushima N, Tanida I, Kominami E, Ohsumi M, Noda T, Ohsumi Y; , Nature. 2000;408:488-492.: A ubiquitin-like system mediates protein lipidation. PUBMED:11100732 EPMC:11100732


This tab holds annotation information from the InterPro database.

InterPro entry IPR007134

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 lysosome/vacuole. Atg3 is a ubiquitin like modifier that is topologically similar to the canonical E2 enzyme [PUBMED:11825910]. It catalyses the conjugation of Atg8 and phosphatidylethanolamine [PUBMED:9023185].

This domain is the N-terminal of Atg3 while the C-terminal is represented by INTERPRO.

Domain organisation

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Alignments

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(104)
Full
(1187)
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(1715)
NCBI
(1845)
Meta
(4)
RP15
(325)
RP35
(640)
RP55
(930)
RP75
(1167)
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  Seed
(104)
Full
(1187)
Representative proteomes UniProt
(1715)
NCBI
(1845)
Meta
(4)
RP15
(325)
RP35
(640)
RP55
(930)
RP75
(1167)
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  Seed
(104)
Full
(1187)
Representative proteomes UniProt
(1715)
NCBI
(1845)
Meta
(4)
RP15
(325)
RP35
(640)
RP55
(930)
RP75
(1167)
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.

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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 View help on the curation process

Seed source: Pfam-B_10019 (release 7.3)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 104
Number in full: 1187
Average length of the domain: 155.40 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 46.35 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.3 20.3
Trusted cut-off 20.4 21.0
Noise cut-off 20.2 19.5
Model length: 137
Family (HMM) version: 13
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Interactions

There are 2 interactions for this family. More...

Autophagy_act_C Autophagy_C

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_N domain has been found. There are 14 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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