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Protein

Autophagy-related protein 3

Gene

ATG3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

E2 conjugating enzyme required for the cytoplasm to vacuole transport (Cvt) and autophagy. Required for selective autophagic degradation of the nucleus (nucleophagy) as well as for mitophagy which contributes to regulate mitochondrial quantity and quality by eliminating the mitochondria to a basal level to fulfill cellular energy requirements and preventing excess ROS production. Responsible for the E2-like covalent binding of phosphatidylethanolamine to the C-terminal Gly of ATG8. The ATG12-ATG5 conjugate plays a role of an E3 and promotes the transfer of ATG8 from ATG3 to phosphatidylethanolamine (PE). This step is required for the membrane association of ATG8. The formation of the ATG8-phosphatidylethanolamine conjugate is essential for autophagy and for the cytoplasm to vacuole transport (Cvt). The ATG8-PE conjugate mediates tethering between adjacent membranes and stimulates membrane hemifusion, leading to expansion of the autophagosomal membrane during autophagy.21 Publications

Enzyme regulationi

ATG12-ATG5 induces reorientation of the ATG3 structure, increasing conjugation activity of ATG3.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei234 – 2341Glycyl thioester intermediateSequence analysis

GO - Molecular functioni

  • Atg8 ligase activity Source: SGD

GO - Biological processi

  • autophagosome assembly Source: UniProtKB
  • C-terminal protein lipidation Source: SGD
  • CVT pathway Source: SGD
  • late nucleophagy Source: SGD
  • mitophagy Source: SGD
  • piecemeal microautophagy of nucleus Source: SGD
  • protein targeting to membrane Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Autophagy, Protein transport, Transport, Ubl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-33325-MONOMER.
ReactomeiR-SCE-1632852. Macroautophagy.

Names & Taxonomyi

Protein namesi
Recommended name:
Autophagy-related protein 3
Alternative name(s):
Autophagy-related E2-like conjugation enzyme ATG3
Gene namesi
Name:ATG3
Synonyms:APG3, AUT1
Ordered Locus Names:YNR007C
ORF Names:N2040
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNR007C.
SGDiS000005290. ATG3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic ubiquitin ligase complex Source: GO_Central
  • cytosol Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi213 – 2131T → A: Decreases ATG8-PE comjugation and autophagy. 1 Publication
Mutagenesisi234 – 2341C → A: Loss of interaction with ATG8 and defect in autophagy and Cvt pathway. 2 Publications
Mutagenesisi234 – 2341C → S: Instead of the formation of an intermediate complex with a thiol ester bond between ATG3 (E2-like enzyme) and ATG8 (substrate), a stable complex with an O-ester bond is formed. 2 Publications
Mutagenesisi270 – 2701W → A: Decreases interaction with ATG8. 1 Publication
Mutagenesisi272 – 2721D → A: Decreases interaction with ATG8. 1 Publication
Mutagenesisi273 – 2731L → A: Decreases interaction with ATG8. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 310310Autophagy-related protein 3PRO_0000213586Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei19 – 191N6-acetyllysine; by ESA11 Publication
Modified residuei48 – 481N6-acetyllysine; by ESA11 Publication

Post-translational modificationi

Acetylated by NuA4 complex acetyltransferase ESA1 at Lys-19 and Lys-48. Acetylation regulates autophagy by controlling ATG8 interaction and lipidation. Deacetylated by histone deacetylase RPD3.2 Publications

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP40344.

Expressioni

Inductioni

Expression is increased during filamentous growth and controlled by the RSF2 transcription factor.2 Publications

Interactioni

Subunit structurei

Monomer. Interacts with ATG8 through an intermediate thioester bond between Cys-234 and the C-terminal Gly of ATG8. Also interacts with the 40 amino acid C-terminal region of the E1-like ATG7 enzyme. Interacts also with the ATG12-ATG5 conjugate.13 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ATG7P388624EBI-3381,EBI-2677
ATG8P381824EBI-3381,EBI-2684

Protein-protein interaction databases

BioGridi35832. 104 interactions.
DIPiDIP-1190N.
IntActiP40344. 10 interactions.
MINTiMINT-389035.

Structurei

Secondary structure

1
310
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi22 – 254Combined sources
Helixi30 – 4314Combined sources
Beta strandi47 – 493Combined sources
Helixi64 – 663Combined sources
Beta strandi69 – 768Combined sources
Turni80 – 823Combined sources
Helixi135 – 1384Combined sources
Beta strandi167 – 17610Combined sources
Turni177 – 1804Combined sources
Beta strandi181 – 19010Combined sources
Helixi198 – 2025Combined sources
Turni207 – 2093Combined sources
Helixi210 – 2134Combined sources
Beta strandi214 – 2185Combined sources
Beta strandi222 – 2243Combined sources
Beta strandi227 – 2315Combined sources
Beta strandi235 – 2373Combined sources
Helixi239 – 26426Combined sources
Helixi283 – 2853Combined sources
Helixi286 – 29712Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DYTX-ray2.50A1-310[»]
3T7GX-ray2.08C/D128-144[»]
4GSLX-ray2.70C/D1-310[»]
ProteinModelPortaliP40344.
SMRiP40344. Positions 21-305.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP40344.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 77PE-binding
Regioni83 – 16381Flexible regionAdd
BLAST
Regioni238 – 28548Handle regionAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi270 – 2734ATG8 interaction motif (AIM)

Domaini

The N-teminal region (residues 1-7) is involved in phosphatidylethanolamine-binding and is required for ATG8-PE conjugation.
The flexible region (FR) is required for ATG7-binding.
The handle region (HR) contains the ATG8 interaction motif (AIM) and mediates binding to ATG8. It is crucial for the cytoplasm-to-vacuole targeting pathway.

Sequence similaritiesi

Belongs to the ATG3 family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000010308.
HOGENOMiHOG000234613.
InParanoidiP40344.
KOiK08343.
OMAiETKEEMH.
OrthoDBiEOG092C3ZYV.

Family and domain databases

InterProiIPR007135. Autophagy-rel_prot_3.
IPR019461. Autophagy-rel_prot_3_C.
IPR007134. Autophagy-rel_prot_3_N.
[Graphical view]
PfamiPF03987. Autophagy_act_C. 1 hit.
PF10381. Autophagy_C. 1 hit.
PF03986. Autophagy_N. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P40344-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIRSTLSSWR EYLTPITHKS TFLTTGQITP EEFVQAGDYL CHMFPTWKWN
60 70 80 90 100
EESSDISYRD FLPKNKQFLI IRKVPCDKRA EQCVEVEGPD VIMKGFAEDG
110 120 130 140 150
DEDDVLEYIG SETEHVQSTP AGGTKDSSID DIDELIQDME IKEEDENDDT
160 170 180 190 200
EEFNAKGGLA KDMAQERYYD LYIAYSTSYR VPKMYIVGFN SNGSPLSPEQ
210 220 230 240 250
MFEDISADYR TKTATIEKLP FYKNSVLSVS IHPCKHANVM KILLDKVRVV
260 270 280 290 300
RQRRRKELQE EQELDGVGDW EDLQDDIDDS LRVDQYLIVF LKFITSVTPS
310
IQHDYTMEGW
Length:310
Mass (Da):35,887
Last modified:February 1, 1995 - v1
Checksum:i52CCFB216B18CF0C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X77395 Genomic DNA. Translation: CAA54575.1.
Z71622 Genomic DNA. Translation: CAA96284.1.
BK006947 Genomic DNA. Translation: DAA10548.1.
PIRiS45130.
RefSeqiNP_014404.3. NM_001183184.3.

Genome annotation databases

EnsemblFungiiYNR007C; YNR007C; YNR007C.
GeneIDi855741.
KEGGisce:YNR007C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X77395 Genomic DNA. Translation: CAA54575.1.
Z71622 Genomic DNA. Translation: CAA96284.1.
BK006947 Genomic DNA. Translation: DAA10548.1.
PIRiS45130.
RefSeqiNP_014404.3. NM_001183184.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DYTX-ray2.50A1-310[»]
3T7GX-ray2.08C/D128-144[»]
4GSLX-ray2.70C/D1-310[»]
ProteinModelPortaliP40344.
SMRiP40344. Positions 21-305.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35832. 104 interactions.
DIPiDIP-1190N.
IntActiP40344. 10 interactions.
MINTiMINT-389035.

Proteomic databases

MaxQBiP40344.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNR007C; YNR007C; YNR007C.
GeneIDi855741.
KEGGisce:YNR007C.

Organism-specific databases

EuPathDBiFungiDB:YNR007C.
SGDiS000005290. ATG3.

Phylogenomic databases

GeneTreeiENSGT00390000010308.
HOGENOMiHOG000234613.
InParanoidiP40344.
KOiK08343.
OMAiETKEEMH.
OrthoDBiEOG092C3ZYV.

Enzyme and pathway databases

BioCyciYEAST:G3O-33325-MONOMER.
ReactomeiR-SCE-1632852. Macroautophagy.

Miscellaneous databases

EvolutionaryTraceiP40344.
PROiP40344.

Family and domain databases

InterProiIPR007135. Autophagy-rel_prot_3.
IPR019461. Autophagy-rel_prot_3_C.
IPR007134. Autophagy-rel_prot_3_N.
[Graphical view]
PfamiPF03987. Autophagy_act_C. 1 hit.
PF10381. Autophagy_C. 1 hit.
PF03986. Autophagy_N. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiATG3_YEAST
AccessioniPrimary (citable) accession number: P40344
Secondary accession number(s): D6W1I2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: September 7, 2016
This is version 140 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 3610 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.