Autophagy-related protein 13 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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Q06628 (ATG13_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 93. 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 13

Gene names

Name:	ATG13
Synonyms:	APG13
Ordered Locus Names:	YPR185W

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	738 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Activates the ATG1 kinase in a nutritional condition dependent manner through the TOR pathway, leading to autophagy. May also be involved in the regulation of autophagy through SNF1. Involved in ATG9 and ATG23 cycling through the pre-autophagosomal structure. Also invoved in cytoplasm to vacuole transport (Cvt) and more specifically in Cvt vesicle formation. Seems to be involved in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage during stationary phase. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.12
Subunit structure	Hypophosphorylated form interacts with ATG1 to form the ATG1 kinase complex. Also interacts with VAC8. Ref.5 Ref.7
Subcellular location	Cytoplasm. Membrane; Peripheral membrane protein Ref.10.
Post-translational modification	Phosphorylated; hyperphosphorylated. Starvation and TOR inactivation results in ATG13 partial dephosphorylation leading to ATG1 binding. Hyperphosphorylation in rich medium is impaired in the absence of VAC8. Ref.7
Miscellaneous	Present with 149 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the ATG13 fungi family.

Ontologies

Keywords
Biological process	Autophagy Protein transport Transport
Cellular component	Cytoplasm Membrane
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	CVT pathway Inferred from mutant phenotype Ref.5. Source: SGD activation of protein kinase activity Inferred from mutant phenotype Ref.7. Source: SGD macroautophagy Inferred from mutant phenotype Ref.1. Source: SGD mitochondrion degradation Inferred from mutant phenotype PubMed 19793921. Source: SGD piecemeal microautophagy of nucleus Inferred from mutant phenotype PubMed 18701704. Source: SGD
Cellular_component	Atg1p signaling complex Inferred from physical interaction PubMed 15743910. Source: SGD extrinsic to membrane Inferred from direct assay Ref.5. Source: SGD
Molecular_function	protein kinase regulator activity Inferred from mutant phenotype Ref.7. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ATG1	P53104	4	EBI-36188,EBI-2657
VAC8	P39968	5	EBI-36188,EBI-20212

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 738

738

Autophagy-related protein 13

PRO_0000157972

Regions

Region

432 – 520

Interaction with ATG1

Compositional bias

306 – 338

Poly-Gln

Compositional bias

622 – 625

Poly-Asp

Compositional bias

699 – 708

Poly-Asn

Amino acid modifications

Modified residue

348

Phosphoserine Ref.16

Modified residue

355

Phosphoserine Ref.14 Ref.16

Modified residue

360

Phosphoserine Ref.14

Modified residue

379

Phosphoserine Ref.16

Modified residue

382

Phosphoserine Ref.16

Modified residue

419

Phosphoserine Ref.16

Modified residue

428

Phosphoserine Ref.13

Modified residue

429

Phosphoserine Ref.16

Modified residue

461

Phosphoserine Ref.16

Modified residue

484

Phosphoserine Ref.16

Modified residue

541

Phosphoserine Ref.16

Modified residue

548

Phosphoserine Ref.16

Modified residue

554

Phosphoserine Ref.15 Ref.16

Modified residue

571

Phosphoserine Ref.16

Modified residue

649

Phosphoserine Ref.13 Ref.16

Modified residue

656

Phosphoserine Ref.16

Sequences

Sequence

Length

Mass (Da)

Tools

Q06628 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 45CD16F69B795E62
Show »

FASTA

738

83,281

        10         20         30         40         50         60 
MVAEEDIEKQ VLQLIDSFFL KTTLLICSTE SSRYQSSTEN IFLFDDTWFE DHSELVSELP 

        70         80         90        100        110        120 
EIISKWSHYD GRKELPPLVV ETYLDLRQLN SSHLVRLKDH EGHLWNVCKG TKKQEIVMER 

       130        140        150        160        170        180 
WLIELDNSSP TFKSYSEDET DVNELSKQLV LLFRYLLTLI QLLPTTELYQ LLIKSYNGPQ 

       190        200        210        220        230        240 
NEGSSNPITS TGPLVSIRTC VLDGSKPILS KGRIGLSKPI INTYSNALNE SNLPAHLDQK 

       250        260        270        280        290        300 
KITPVWTKFG LLRVSVSYRR DWKFEINNTN DELFSARHAS VSHNSQGPQN QPEQEGQSDQ 

       310        320        330        340        350        360 
DIGKRQPQFQ QQQQPQQQQQ QQQQQQRQHQ VQTQQQRQIP DRRSLSLSPC TRANSFEPQS 

       370        380        390        400        410        420 
WQKKVYPISR PVQPFKVGSI GSQSASRNPS NSSFFNQPPV HRPSMSSNYG PQMNIEGTSV 

       430        440        450        460        470        480 
GSTSKYSSSF GNIRRHSSVK TTENAEKVSK AVKSPLQPQE SQEDLMDFVK LLEEKPDLTI 

       490        500        510        520        530        540 
KKTSGNNPPN INISDSLIRY QNLKPSNDLL SEDLSVSLSM DPNHTYHRGR SDSHSPLPSI 

       550        560        570        580        590        600 
SPSMHYGSLN SRMSQGANAS HLIARGGGNS STSALNSRRN SLDKSSNKQG MSGLPPIFGG 

       610        620        630        640        650        660 
ESTSYHHDNK IQKYNQLGVE EDDDDENDRL LNQMGNSATK FKSSISPRSI DSISSSFIKS 

       670        680        690        700        710        720 
RIPIRQPYHY SQPTTAPFQA QAKFHKPANK LIDNGNRSNS NNNNHNGNDA VGVMHNDEDD 

       730 
QDDDLVFFMS DMNLSKEG

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Analyses of APG13 gene involved in autophagy in yeast, Saccharomyces cerevisiae." Funakoshi T., Matsuura A., Noda T., Ohsumi Y. Gene 192:207-213(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"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. Hani J. Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"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.
[5]	"Apg13p and Vac8p are part of a complex of phosphoproteins that are required for cytoplasm to vacuole targeting." Scott S.V., Nice D.C. III, Nau J.J., Weisman L.S., Kamada Y., Keizer-Gunnink I., Funakoshi T., Veenhuis M., Ohsumi Y., Klionsky D.J. J. Biol. Chem. 275:25840-25849(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH VAC8.
[6]	"Dissection of autophagosome biogenesis into distinct nucleation and expansion steps." Abeliovich H., Dunn W.A. Jr., Kim J., Klionsky D.J. J. Cell Biol. 151:1025-1034(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Tor-mediated induction of autophagy via an Apg1 protein kinase complex." Kamada Y., Funakoshi T., Shintani T., Nagano K., Ohsumi M., Ohsumi Y. J. Cell Biol. 150:1507-1513(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, PHOSPHORYLATION, INTERACTION WITH ATG1.
[8]	"Antagonistic controls of autophagy and glycogen accumulation by Snf1p, the yeast homolog of AMP-activated protein kinase, and the cyclin-dependent kinase Pho85p." Wang Z., Wilson W.A., Fujino M.A., Roach P.J. Mol. Cell. Biol. 21:5742-5752(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[12]	"The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure." Reggiori F., Tucker K.A., Stromhaug P.E., Klionsky D.J. Dev. Cell 6:79-90(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[13]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-428 AND SER-649, MASS SPECTROMETRY. Strain: YAL6B.
[14]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-355 AND SER-360, MASS SPECTROMETRY. Strain: ADR376.
[15]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-554, MASS SPECTROMETRY.
[16]	"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-348; SER-355; SER-379; SER-382; SER-419; SER-429; SER-461; SER-484; SER-541; SER-548; SER-554; SER-571; SER-649 AND SER-656, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U25842 Genomic DNA. Translation: AAB68118.1. D88025 Genomic DNA. Translation: BAA21485.1. BK006949 Genomic DNA. Translation: DAA11601.1.
PIR	S59842.
RefSeq	NP_015511.1. NM_001184282.1.
3D structure databases
ProteinModelPortal	Q06628.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-1191N.
IntAct	Q06628. 7 interactions.
MINT	MINT-384768.
STRING	4932.YPR185W.
Proteomic databases
PaxDb	Q06628.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YPR185W; YPR185W; YPR185W.
GeneID	856315.
KEGG	sce:YPR185W.
Organism-specific databases
CYGD	YPR185w.
SGD	S000006389. ATG13.
Phylogenomic databases
eggNOG	NOG318247.
GeneTree	ENSGT00700000105971.
HOGENOM	HOG000034130.
KO	K08331.
OMA	RWLVELD.
OrthoDB	EOG490BKF.
Gene expression databases
Genevestigator	Q06628.
GermOnline	YPR185W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR018731. Autophagy-rel_p13. [Graphical view]
Pfam	PF10033. ATG13. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	981697.

Entry information

Entry name

ATG13_YEAST

Accession

Primary (citable) accession number: Q06628
Secondary accession number(s): D6W4I5

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2005
Last sequence update:	November 1, 1996
Last modified:	April 3, 2013
This is version 93 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 XVI

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

Uncharacterized protein families (UPF)

List of uncharacterized protein family (UPF) entries

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

Regions

Amino acid modifications

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