Autophagy-related protein 3 - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot P40344 (ATG3_YEAST)

Last modified January 19, 2010. Version 82. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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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 (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

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

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Protein attributes

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

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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.4 Ref.5 Ref.6 Ref.8 Ref.12
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.6 Ref.7
Subcellular location	Cytoplasm Ref.8 Ref.10.
Miscellaneous	Present with 3610 molecules/cell in log phase SD medium. Ref.11
Sequence similarities	Belongs to the ATG3 family.

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Ontologies

Keywords
Biological process	Autophagy Protein transport Transport Ubl conjugation pathway
Cellular component	Cytoplasm
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	C-terminal protein lipidation Ref.6 Ref.12 Inferred from direct assay. Source: SGD CVT pathway Ref.1 Inferred from mutant phenotype. Source: SGD autophagic vacuole assembly Ref.8 Inferred from mutant phenotype. Source: UniProtKB modification-dependent protein catabolic process Inferred from electronic annotation. Source: UniProtKB-KW piecemeal microautophagy of nucleus Inferred from mutant phenotype. Source: SGD protein targeting to membrane Ref.8 Inferred from mutant phenotype. Source: UniProtKB
Cellular component	cytosol Ref.8 Inferred from direct assay. Source: UniProtKB
Molecular function	Atg8 ligase activity Ref.6 Inferred from mutant phenotype. Source: SGD identical protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
itself		1	EBI-3381,EBI-3381
ATG7	P38862	4	EBI-3381,EBI-2677
ATG8	P38182	1	EBI-3381,EBI-2684

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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.6 Ref.12

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.6 Ref.12

Secondary structure

310

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P40344-1 [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

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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: 9023185] [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: 7900425] [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: 9169873] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	"Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae." Tsukada M., Ohsumi Y. FEBS Lett. 333:169-174(1993) [PubMed: 8224160] [Abstract] Cited for: FUNCTION.
[5]	"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: 8050581] [Abstract] Cited for: FUNCTION.
[6]	"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: 11100732] [Abstract] Cited for: FUNCTION, INTERACTION WITH ATG8, MUTAGENESIS OF CYS-234.
[7]	"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: 11139573] [Abstract] Cited for: INTERACTION WITH ATG7.
[8]	"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: 11149920] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[9]	"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: 14536056] [Abstract] Cited for: NOMENCLATURE.
[10]	"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: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[11]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[12]	"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: 15277523] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF CYS-234.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

PIR

S45130.

RefSeq

NP_014404.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2DYT	X-ray	2.50	A	1-310	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1190N.

IntAct

P40344. 13 interactions.

STRING

P40344.

Proteomic databases

PeptideAtlas

P40344.

Genome annotation databases

Ensembl

YNR007C; YNR007C; YNR007C; Saccharomyces cerevisiae. [Genome view]

GeneID

855741.

KEGG

sce:YNR007C.

NMPDR

fig|4932.3.peg.5484.

Organism-specific databases

CYGD

YNR007c.

SGD

S000005290. ATG3.

Phylogenomic databases

eggNOG

HOGENOM

OMA

OrthoDB

PhylomeDB

P40344.

Gene expression databases

ArrayExpress

P40344.

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 Resources

NextBio

980136.

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Entry information

Entry name

ATG3_YEAST

Accession

Primary (citable) accession number: P40344

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	January 19, 2010
This is version 82 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Yeast

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

Yeast chromosome XIV

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

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

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents