Autophagy-related protein 3 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P40344 (ATG3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 112. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Autophagy-related protein 3

Alternative name(s):
Autophagy-related E2-like conjugation enzyme ATG3

Gene names

Name:	ATG3
Synonyms:	APG3, AUT1
Ordered Locus Names:	YNR007C
ORF Names:	N2040

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	310 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	E2 conjugating enzyme responsible for the E2-like covalent binding of phosphatidylethanolamine to the C-terminal Gly of ATG8. 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). Ref.1 Ref.5 Ref.6 Ref.7 Ref.9 Ref.13
Subunit structure	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. Ref.7 Ref.8
Subcellular location	Cytoplasm Ref.9 Ref.11.
Miscellaneous	Present with 3610 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the ATG3 family.

Ontologies

Keywords
Biological process	Autophagy Protein transport Transport Ubl conjugation pathway
Cellular component	Cytoplasm
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	C-terminal protein lipidation Inferred from direct assay Ref.13. Source: SGD CVT pathway Inferred from mutant phenotype Ref.1. Source: SGD autophagic vacuole assembly Inferred from mutant phenotype Ref.9. Source: UniProtKB mitochondrion degradation Inferred from mutant phenotype PubMed 19793921. Source: SGD piecemeal microautophagy of nucleus Inferred from mutant phenotype PubMed 18701704. Source: SGD protein targeting to membrane Inferred from mutant phenotype Ref.9. Source: UniProtKB
Cellular_component	cytosol Inferred from direct assay Ref.9. Source: UniProtKB
Molecular_function	Atg8 ligase activity Inferred from mutant phenotype Ref.7. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ATG7	P38862	4	EBI-3381,EBI-2677

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 310

310

Autophagy-related protein 3

PRO_0000213586

Sites

Active site

234

Glycyl thioester intermediate Potential

Experimental info

Mutagenesis

234

C → A: Loss of interaction with ATG8 and defect in autophagy and Cvt pathway. Ref.7 Ref.13

Mutagenesis

234

C → 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. Ref.7 Ref.13

Secondary structure

310

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P40344 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: 52CCFB216B18CF0C
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FASTA

310

35,887

        10         20         30         40         50         60 
MIRSTLSSWR EYLTPITHKS TFLTTGQITP EEFVQAGDYL CHMFPTWKWN EESSDISYRD 

        70         80         90        100        110        120 
FLPKNKQFLI IRKVPCDKRA EQCVEVEGPD VIMKGFAEDG DEDDVLEYIG SETEHVQSTP 

       130        140        150        160        170        180 
AGGTKDSSID DIDELIQDME IKEEDENDDT EEFNAKGGLA KDMAQERYYD LYIAYSTSYR 

       190        200        210        220        230        240 
VPKMYIVGFN SNGSPLSPEQ MFEDISADYR TKTATIEKLP FYKNSVLSVS IHPCKHANVM 

       250        260        270        280        290        300 
KILLDKVRVV RQRRRKELQE EQELDGVGDW EDLQDDIDDS LRVDQYLIVF LKFITSVTPS 

       310 
IQHDYTMEGW

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"AUT1, a gene essential for autophagocytosis in the yeast Saccharomyces cerevisiae." Schlumpberger M., Schaeffeler E., Straub M., Bredschneider M., Wolf D.H., Thumm M. J. Bacteriol. 179:1068-1076(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	"Twelve open reading frames revealed in the 23.6 kb segment flanking the centromere on the Saccharomyces cerevisiae chromosome XIV right arm." Verhasselt P., Aert R., Voet M., Volckaert G. Yeast 10:1355-1361(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications." Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. Hani J. Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae." Tsukada M., Ohsumi Y. FEBS Lett. 333:169-174(1993) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[6]	"Isolation of autophagocytosis mutants of Saccharomyces cerevisiae." Thumm M., Egner R., Koch B., Schlumpberger M., Straub M., Veenhuis M., Wolf D.H. FEBS Lett. 349:275-280(1994) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"A ubiquitin-like system mediates protein lipidation." 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 408:488-492(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH ATG8, MUTAGENESIS OF CYS-234.
[8]	"The C-terminal region of an Apg7p/Cvt2p is required for homodimerization and is essential for its E1 activity and E1-E2 complex formation." Komatsu M., Tanida I., Ueno T., Ohsumi M., Ohsumi Y., Kominami E. J. Biol. Chem. 276:9846-9854(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ATG7.
[9]	"Membrane recruitment of Aut7p in the autophagy and cytoplasm to vacuole targeting pathways requires Aut1p, Aut2p, and the autophagy conjugation complex." Kim J., Huang W.-P., Klionsky D.J. J. Cell Biol. 152:51-64(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[10]	"A unified nomenclature for yeast autophagy-related genes." Klionsky D.J., Cregg J.M., Dunn W.A. Jr., Emr S.D., Sakai Y., Sandoval I.V., Sibirny A., Subramani S., Thumm M., Veenhuis M., Ohsumi Y. Dev. Cell 5:539-545(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NOMENCLATURE.
[11]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[12]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[13]	"In vivo and in vitro reconstitution of atg8 conjugation essential for autophagy." Ichimura Y., Imamura Y., Emoto K., Umeda M., Noda T., Ohsumi Y. J. Biol. Chem. 279:40584-40592(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF CYS-234.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X77395 Genomic DNA. Translation: CAA54575.1.
Z71622 Genomic DNA. Translation: CAA96284.1.
BK006947 Genomic DNA. Translation: DAA10548.1.

PIR

S45130.

RefSeq

NP_014404.3. NM_001183184.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2DYT	X-ray	2.50	A	1-310	[»]
3T7G	X-ray	2.08	C/D	128-144	[»]
4GSL	X-ray	2.70	C/D	1-310	[»]

SMR

P40344. Positions 21-305.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1190N.

IntAct

P40344. 8 interactions.

MINT

MINT-389035.

STRING

4932.YNR007C.

Proteomic databases

PaxDb

P40344.

PeptideAtlas

P40344.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YNR007C; YNR007C; YNR007C.

GeneID

855741.

KEGG

sce:YNR007C.
sce:YNR014W.

Organism-specific databases

CYGD

YNR007c.

SGD

S000005290. ATG3.

Phylogenomic databases

eggNOG

NOG237080.

GeneTree

ENSGT00390000010308.

HOGENOM

HOG000234613.

K08343.

OMA

MLLQPEL.

OrthoDB

EOG4F21CM.

Gene expression databases

Genevestigator

P40344.

GermOnline

YNR007C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR007135. Autophagy-rel_prot_3.
IPR019461. Autophagy-rel_prot_3_C.
IPR007134. Autophagy-rel_prot_3_N.
[Graphical view]

Pfam

PF03987. Autophagy_act_C. 1 hit.
PF10381. Autophagy_Cterm. 1 hit.
PF03986. Autophagy_N. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P40344.

NextBio

980136.

Entry information

Entry name

ATG3_YEAST

Accession

Primary (citable) accession number: P40344
Secondary accession number(s): D6W1I2

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	May 1, 2013
This is version 112 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome XIV

Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents