P38316 (ATG12_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin-like protein ATG12

Alternative name(s):
Autophagy-related protein 12

Gene names

Name:	ATG12
Synonyms:	APG12
Ordered Locus Names:	YBR217W
ORF Names:	YBR1506

Organism

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

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	186 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Ubiquitin-like protein involved in cytoplasm to vacuole transport (Cvt), autophagy vesicles formation, mitophagy, and nucleophagy. Conjugation with ATG5 through an ubiquitin-like conjugating system involving also ATG7 as an E1-like activating enzyme and ATG10 as an E2-like conjugating enzyme, is essential for its function. The ATG12-ATG5 conjugate acts as an E3-like enzyme which is required for lipidation of ATG8 and ATG8 association to the vesicle membranes. ATG12-ATG5 rearranges the ATG3 catalytic center and enhances its E2 activity. Ref.1 Ref.5 Ref.11
Subunit structure	Forms a conjugate with ATG5. Forms a thioester bond with the 'Cys-133' of ATG10. Interacts with the ATG7 C-terminal 40 amino acids domain. The ATG12-ATG5 conjugate forms a complex with several units of ATG16. The ATG12-ATG5 conjugate associates also with ATG3. Interacts with COG2.
Subcellular location	Preautophagosomal structure membrane; Peripheral membrane protein. Note: Localizes to the isolation membrane (IM), a membrane sac which is generated from the pre-autophagosomal structure (PAS). Ultimately, the IM expands to become a mature autophagosome. Localizes also to a dot at the junction between the IM and the vacuolar membrane, termed the vacuole-IM contact site (VICS).
Miscellaneous	Small amount of ATG5-ATG12 conjugate is enough to perform normal autophagy.
Sequence similarities	Belongs to the ATG12 family.

Ontologies

Keywords
Biological process	Autophagy Protein transport Transport Ubl conjugation pathway
Cellular component	Membrane
PTM	Isopeptide bond Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	C-terminal protein lipidation Inferred from direct assay Ref.19. Source: SGD CVT pathway Inferred from mutant phenotype Ref.1. Source: SGD autophagic vacuole assembly Inferred from mutant phenotype Ref.15. Source: SGD mitochondrion degradation Inferred from mutant phenotype PubMed 19793921. Source: SGD piecemeal microautophagy of nucleus Inferred from mutant phenotype Ref.23. Source: SGD
Cellular_component	Atg12-Atg5-Atg16 complex Inferred from direct assay Ref.12. Source: SGD pre-autophagosomal structure Inferred by curator Ref.12. Source: SGD
Molecular_function	protein tag Inferred from physical interaction Ref.7Ref.6Ref.1. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ATG16	Q03818	10	EBI-2692,EBI-27344
ATG5	Q12380	8	EBI-2692,EBI-2664
ATG7	P38862	3	EBI-2692,EBI-2677

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 186

186

Ubiquitin-like protein ATG12

PRO_0000212485

Amino acid modifications

Modified residue

55

1

Phosphoserine Ref.24

Cross-link

186

Glycyl lysine isopeptide (Gly-Lys) (interchain with K-149 in ATG5)

Experimental info

Mutagenesis

106

1

I → A: Decreases protein stability.

Mutagenesis

108

1

F → A: Decreases protein stability.

Mutagenesis

149

1

Y → A: Impairs conjugation to ATG5 and autophagic activity.

Mutagenesis

154

1

F → A: Impairs conjugation to ATG5 and autophagic activity.

Mutagenesis

186

1

G → A: Strong decrease of conjugation with ATG5. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

186

Helix Strand Turn

Details...

Beta strand

103 – 110

8

Beta strand

121 – 125

5

Helix

130 – 141

12

Beta strand

147 – 150

4

Turn

151 – 153

3

Helix

162 – 169

8

Beta strand

174 – 180

7

Sequences

	Sequence		Length	Mass (Da)
	P38316 [UniParc]. Last modified October 1, 1994. Version 1. Checksum: 74B3C9FD3CEA9265	FASTA	186	21,106
	10 20 30 40 50 60 MSRILESENE TESDESSIIS TNNGTAMERS RNNQELRSSP HTVQNRLELF SRRLSQLGLA 70 80 90 100 110 120 SDISVDQQVE DSSSGTYEQE ETIKTNAQTS KQKSHKDEKN IQKIQIKFQP IGSIGQLKPS 130 140 150 160 170 180 VCKISMSQSF AMVILFLKRR LKMDHVYCYI NNSFAPSPQQ NIGELWMQFK TNDELIVSYC ASVAFG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, PHOSPHORYLATION, CONJUGATION TO ATG5, SUBCELLULAR LOCATION, MUTAGENESIS OF GLY-186. Strain: ATCC 26109 / X2180.
[2]	"Complete DNA sequence of yeast chromosome II." Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K. EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. 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]	"Apg10p, a novel protein-conjugating enzyme essential for autophagy in yeast." Shintani T., Mizushima N., Ogawa Y., Matsuura A., Noda T., Ohsumi Y. EMBO J. 18:5234-5241(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ATG10.
[7]	"Apg7p/Cvt2p: a novel protein-activating enzyme essential for autophagy." Tanida I., Mizushima N., Kiyooka M., Ohsumi M., Ueno T., Ohsumi Y., Kominami E. Mol. Biol. Cell 10:1367-1379(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ATG7.
[8]	"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] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ATG5, SUBCELLULAR LOCATION.
[9]	"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] [Europe PMC] [Abstract] Cited for: FUNCTION.
[10]	"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.
[11]	"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.
[12]	"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] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN A COMPLEX WITH ATG5 AND ATG16.
[13]	"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.
[14]	"The carboxyl terminal 17 amino acids within Apg7 are essential for Apg8 lipidation, but not for Apg12 conjugation." Yamazaki-Sato H., Tanida I., Ueno T., Kominami E. FEBS Lett. 551:71-77(2003) [PubMed] [Europe PMC] [Abstract] Cited for: CONJUGATION TO ATG5.
[15]	"Structure-function relationship of Atg12, a ubiquitin-like modifier essential for autophagy." Hanada T., Ohsumi Y. Autophagy 1:110-118(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CONJUGATION TO ATG5, MUTAGENESIS OF ILE-106; PHE-108; TYR-149 AND PHE-154.
[16]	"Endoplasmic reticulum stress triggers autophagy." Yorimitsu T., Nair U., Yang Z., Klionsky D.J. J. Biol. Chem. 281:30299-30304(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[17]	"The role of autophagy in mitochondria maintenance: characterization of mitochondrial functions in autophagy-deficient S. cerevisiae strains." Zhang Y., Qi H., Taylor R., Xu W., Liu L.F., Jin S. Autophagy 3:337-346(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[18]	"Hierarchy of Atg proteins in pre-autophagosomal structure organization." Suzuki K., Kubota Y., Sekito T., Ohsumi Y. Genes Cells 12:209-218(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[19]	"The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy." Hanada T., Noda N.N., Satomi Y., Ichimura Y., Fujioka Y., Takao T., Inagaki F., Ohsumi Y. J. Biol. Chem. 282:37298-37302(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE ATG12-ATG5 CONJUGATE, INTERACTION WITH ATG3.
[20]	"New insights into autophagy using a multiple knockout strain." Cao Y., Klionsky D.J. Autophagy 4:1073-1075(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[21]	"In vivo reconstitution of autophagy in Saccharomyces cerevisiae." Cao Y., Cheong H., Song H., Klionsky D.J. J. Cell Biol. 182:703-713(2008) [PubMed] [Europe PMC] [Abstract] Cited for: CONJUGATION TO ATG5, FUNCTION OF THE ATG12-ATG5 CONJUGATE.
[22]	"Crystallization of the Atg12-Atg5 conjugate bound to Atg16 by the free-interface diffusion method." Noda N.N., Fujioka Y., Ohsumi Y., Inagaki F. J. Synchrotron Radiat. 15:266-268(2008) [PubMed] [Europe PMC] [Abstract] Cited for: CRYSTALLIZATION OF THE ATG12-ATG5 CONJUGATE BOUND TO ATG16.
[23]	"Piecemeal microautophagy of the nucleus requires the core macroautophagy genes." Krick R., Muehe Y., Prick T., Bremer S., Schlotterhose P., Eskelinen E.L., Millen J., Goldfarb D.S., Thumm M. Mol. Biol. Cell 19:4492-4505(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[24]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-55, MASS SPECTROMETRY.
[25]	"The conserved oligomeric Golgi complex is involved in double-membrane vesicle formation during autophagy." Yen W.L., Shintani T., Nair U., Cao Y., Richardson B.C., Li Z., Hughson F.M., Baba M., Klionsky D.J. J. Cell Biol. 188:101-114(2010) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH COG2.
[26]	"Sphingolipid synthesis is involved in autophagy in Saccharomyces cerevisiae." Yamagata M., Obara K., Kihara A. Biochem. Biophys. Res. Commun. 410:786-791(2011) [PubMed] [Europe PMC] [Abstract] Cited for: CONJUGATION TO ATG5.
[27]	"Mechanism and functions of membrane binding by the Atg5-Atg12/Atg16 complex during autophagosome formation." Romanov J., Walczak M., Ibiricu I., Schuchner S., Ogris E., Kraft C., Martens S. EMBO J. 31:4304-4317(2012) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, FUNCTION OF THE ATG5-ATG12/ATG16 COMPLEX.
[28]	"A late form of nucleophagy in Saccharomyces cerevisiae." Mijaljica D., Prescott M., Devenish R.J. PLoS ONE 7:E40013-E40013(2012) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[29]	"Fine mapping of autophagy-related proteins during autophagosome formation in Saccharomyces cerevisiae." Suzuki K., Akioka M., Kondo-Kakuta C., Yamamoto H., Ohsumi Y. J. Cell Sci. 0:0-0(2013) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[30]	"Structure of the Atg12-Atg5 conjugate reveals a platform for stimulating Atg8-PE conjugation." Noda N.N., Fujioka Y., Hanada T., Ohsumi Y., Inagaki F. EMBO Rep. 14:206-211(2013) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 100-186 IN CONJUGATION WITH ATG5.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB017924 Genomic DNA. Translation: BAA33473.1.
Z36086 Genomic DNA. Translation: CAA85181.1.
AY557706 Genomic DNA. Translation: AAS56032.1.
BK006936 Genomic DNA. Translation: DAA07333.1.

PIR

S46093.

RefSeq

NP_009776.1. NM_001178565.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3W1S	X-ray	2.60	C	100-186	[»]

ProteinModelPortal

P38316.

SMR

P38316. Positions 101-181.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1189N.

IntAct

P38316. 105 interactions.

MINT

MINT-388309.

STRING

4932.YBR217W.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YBR217W; YBR217W; YBR217W.

GeneID

852518.

KEGG

sce:YBR217W.

Organism-specific databases

CYGD

YBR217w.

SGD

S000000421. ATG12.

Phylogenomic databases

eggNOG

NOG236266.

GeneTree

ENSGT00390000016654.

HOGENOM

HOG000234863.

KO

K08336.

OMA

ELIVSYC.

OrthoDB

EOG4B2X6W.

Enzyme and pathway databases

BioCyc

YEAST:G3O-29154-MONOMER.

Gene expression databases

Genevestigator

P38316.

GermOnline

YBR217W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR007242. Atg12.
[Graphical view]

PANTHER

PTHR13385. PTHR13385. 1 hit.

Pfam

PF04110. APG12. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

971550.

Entry information

Entry name

ATG12_YEAST

Accession

Primary (citable) accession number: P38316
Secondary accession number(s): D6VQL3

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	October 1, 1994
Last modified:	May 29, 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