Reviewed, UniProtKB/Swiss-Prot Q12380 (ATG5_YEAST)

Names and origin

Protein names

Recommended name:
    Autophagy protein 5

Gene names

Name:	ATG5
Synonyms:	APG5
Ordered Locus Names:	YPL149W
ORF Names:	P2601

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	294 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Involved in cytoplasm to vacuole transport (Cvt) and autophagy vesicles formation. Required for ATG8 association to the vesicle membranes. Ref.1 Ref.4 Ref.5 Ref.6 Ref.7 Ref.9
Subunit structure	Conjugated with ATG12. The ATG5-ATG12 conjugate forms a complex with several units of ATG16.
Subcellular location	Cytoplasm. Membrane; Peripheral membrane protein. Preautophagosomal structure membrane; Peripheral membrane protein. Note: Found in pre-autophagosomal structure and other punctate structures. Ref.8
Post-translational modification	Conjugated to ATG12; which is essential for autophagy. Conjugation with ATG12 involves ATG7 as an E1-like activating enzyme and ATG10 as an E2-like conjugating enzyme.
Miscellaneous	Present with 606 molecules/cell in log phase SD medium. Ref.12 Small amount of ATG5-ATG12 conjugate is enough to perform normal autophagy.
Sequence similarities	Belongs to the ATG5 family.

Ontologies

Keywords
Biological process	Autophagy Protein transport Transport
Cellular component	Cytoplasm Membrane
Molecular function	Hydrolase
PTM	Isopeptide bond Ubl conjugation
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	C-terminal protein lipidation Inferred from direct assay. Source: SGD CVT pathway Ref.7 Inferred from mutant phenotype. Source: SGD macroautophagy Ref.1 Inferred from mutant phenotype. Source: SGD piecemeal microautophagy of nucleus Inferred from mutant phenotype. Source: SGD
Cellular component	Atg12-Atg5-Atg16 complex Ref.10 Inferred from direct assay. Source: SGD autophagic vacuole Inferred from direct assay. Source: SGD cytosol Ref.10 Inferred from direct assay. Source: SGD extrinsic to membrane Inferred from electronic annotation. Source: UniProtKB-SubCell pre-autophagosomal structure Ref.8 Inferred from direct assay. Source: SGD
Molecular function	hydrolase activity Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ATG12	P38316	1	EBI-2664,EBI-2692
ATG16	Q03818	3	EBI-2664,EBI-27344

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 294

294

Autophagy protein 5

PRO_0000219010

Amino acid modifications

Cross-link

149

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ATG12)

Experimental info

Mutagenesis

149

1

K → R: Loss of conjugation. Ref.5

Secondary structure

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294

Helix Strand Turn

Details...

Helix

1 – 9

9

Beta strand

12 – 19

8

Helix

21 – 23

3

Helix

30 – 33

4

Beta strand

34 – 43

10

Helix

45 – 48

4

Helix

49 – 56

8

Helix

57 – 59

3

Beta strand

60 – 62

3

Beta strand

71 – 76

6

Beta strand

79 – 81

3

Helix

87 – 95

9

Helix

96 – 98

3

Beta strand

110 – 125

16

Helix

139 – 156

18

Beta strand

157 – 159

3

Helix

160 – 163

4

Helix

167 – 179

13

Helix

182 – 192

11

Beta strand

202 – 205

4

Beta strand

208 – 212

5

Helix

230 – 232

3

Helix

233 – 236

4

Turn

239 – 241

3

Beta strand

248 – 252

5

Beta strand

255 – 257

3

Helix

263 – 270

8

Beta strand

277 – 283

7

Sequences

	Sequence		Length	Mass (Da)
	Q12380-1 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: BE513A631DEAA0A1	FASTA	294	33,560
	10 20 30 40 50 60 MNDIKQLLWN GELNVLVSID PSFLMKGSPR EIAVLRIRVP RETYLVNYMP LIWNKIKSFL 70 80 90 100 110 120 SFDPLTDSEK YFWFEHNKTP IPWNYPVGVL FDCLAGKSAT FTTSFENQVK DVLTFLRIHL 130 140 150 160 170 180 VMGDSLPPTI IPIASSKTQA EKFWFHQWKQ VCFILNGSSK AIMSLSVNEA RKFWGSVITR 190 200 210 220 230 240 NFQDFIEISN KISSSRPRHI PLIIQTSRTS GTFRISQPTI SMTGVNPTLK DIEGDILDVK 250 260 270 280 290 EGINGNDVMV ICQGIEIPWH MLLYDLYSKL RSFDGFLYIT LVPIKGGDKA SSEL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structural and functional analyses of APG5, a gene involved in autophagy in yeast." Kametaka S., Matsuura A., Wada Y., Ohsumi Y. Gene 178:139-143(1996) [PubMed: 8921905] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	"The sequence of 55 kb on the left arm of yeast chromosome XVI identifies a small nuclear RNA, a new putative protein kinase and two new putative regulators." Purnelle B., Coster F., Goffeau A. Yeast 12:1483-1492(1996) [PubMed: 8948103] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI." Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M. , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J. Nature 387:103-105(1997) [PubMed: 9169875] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[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]	"A protein conjugation system essential for autophagy." Mizushima N., Noda T., Yoshimori T., Tanaka Y., Ishii T., George M.D., Klionsky D.J., Ohsumi M., Ohsumi Y. Nature 395:395-398(1998) [PubMed: 9759731] [Abstract] Cited for: FUNCTION, CONJUGATION TO ATG12, MUTAGENESIS OF LYS-149. Strain: ATCC 26109 / X2180.
[6]	"Apg16p is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway." Mizushima N., Noda T., Ohsumi Y. EMBO J. 18:3888-3896(1999) [PubMed: 10406794] [Abstract] Cited for: FUNCTION, INTERACTION WITH ATG12 AND ATG16.
[7]	"Apg5p functions in the sequestration step in the cytoplasm-to-vacuole targeting and macroautophagy pathways." George M.D., Baba M., Scott S.V., Mizushima N., Garrison B.S., Ohsumi Y., Klionsky D.J. Mol. Biol. Cell 11:969-982(2000) [PubMed: 10712513] [Abstract] Cited for: FUNCTION.
[8]	"The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation." Suzuki K., Kirisako T., Kamada Y., Mizushima N., Noda T., Ohsumi Y. EMBO J. 20:5971-5981(2001) [PubMed: 11689437] [Abstract] Cited for: SUBCELLULAR LOCATION.
[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: 11149920] [Abstract] Cited for: FUNCTION.
[10]	"Formation of the approximately 350-kDa Apg12-Apg5.Apg16 multimeric complex, mediated by Apg16 oligomerization, is essential for autophagy in yeast." Kuma A., Mizushima N., Ishihara N., Ohsumi Y. J. Biol. Chem. 277:18619-18625(2002) [PubMed: 11897782] [Abstract] Cited for: IDENTIFICATION IN A COMPLEX WITH ATG12 AND ATG16.
[11]	"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.
[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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

D83519 Genomic DNA. Translation: BAA11937.1.
X96770 Genomic DNA. Translation: CAA65572.1.
Z73505 Genomic DNA. Translation: CAA97854.1.

PIR

S65160.

RefSeq

NP_015176.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2DYM	X-ray	2.20	A/C/E/G	1-294	[»]
2DYO	X-ray	1.97	A	1-294	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:1195N.

IntAct

Q12380. 10 interactions.

STRING

Q12380.

Genome annotation databases

Ensembl

YPL149W; YPL149W; YPL149W; Saccharomyces cerevisiae. [Genome view]

GeneID

855954.

KEGG

sce:YPL149W.

NMPDR

fig|4932.3.peg.6306.

Organism-specific databases

CYGD

YPL149w.

SGD

S000006070. ATG5.

Phylogenomic databases

HOGENOM

Q12380.

OMA

PRESHIA

OrthoDB

EOG9WSXTH

Gene expression databases

ArrayExpress

Q12380.

Genevestigator

Q12380.

GermOnline

YPL149W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR007239. Autophagy-rel_prot_5.
[Graphical view]

PANTHER

PTHR13040. APG5. 1 hit.

Pfam

PF04106. APG5. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

980741.

Entry information

Entry name

ATG5_YEAST

Accession

Primary (citable) accession number: Q12380

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	November 24, 2009
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)