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Protein

Guanine nucleotide-exchange factor SEC12

Gene

SEC12

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Guanine nucleotide-exchange factor (GEF) required for the formation or budding of transport vesicles from the ER. This function involves the cytoplasmic domain of the protein, which is thought to interact with the small GTP-binding protein SAR1. Required for autophagy.16 Publications

GO - Molecular functioni

GO - Biological processi

  • protein transport Source: UniProtKB-KW
  • regulation of COPII vesicle coating Source: SGD
  • vesicle-mediated transport Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

GTPase activation

Keywords - Biological processi

ER-Golgi transport, Protein transport, Transport

Enzyme and pathway databases

BioCyciYEAST:G3O-33339-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Guanine nucleotide-exchange factor SEC12
Alternative name(s):
Protein transport protein SEC12
Gene namesi
Name:SEC12
Synonyms:SED2
Ordered Locus Names:YNR026C
ORF Names:N3244
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNR026C.
SGDiS000005309. SEC12.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 354354Cytoplasmic1 PublicationAdd
BLAST
Transmembranei355 – 37319Helical; Signal-anchor for type II membrane proteinAdd
BLAST
Topological domaini374 – 47198Lumenal1 PublicationAdd
BLAST

GO - Cellular componenti

  • endoplasmic reticulum Source: SGD
  • endoplasmic reticulum membrane Source: UniProtKB-SubCell
  • Golgi apparatus Source: SGD
  • integral component of membrane Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Golgi apparatus, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 471471Guanine nucleotide-exchange factor SEC12PRO_0000097657Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi439 – 4391N-linked (GlcNAc...)Sequence analysis
Glycosylationi462 – 4621N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

MaxQBiP11655.

Interactioni

Protein-protein interaction databases

BioGridi35850. 53 interactions.
DIPiDIP-7541N.
IntActiP11655. 2 interactions.
MINTiMINT-1356711.

Structurei

Secondary structure

1
471
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 95Combined sources
Beta strandi14 – 218Combined sources
Beta strandi24 – 307Combined sources
Beta strandi33 – 375Combined sources
Beta strandi40 – 478Combined sources
Beta strandi51 – 533Combined sources
Helixi54 – 574Combined sources
Beta strandi58 – 658Combined sources
Beta strandi75 – 795Combined sources
Beta strandi82 – 865Combined sources
Helixi91 – 966Combined sources
Beta strandi103 – 1097Combined sources
Turni110 – 1134Combined sources
Beta strandi114 – 1218Combined sources
Beta strandi133 – 1386Combined sources
Beta strandi145 – 1506Combined sources
Beta strandi155 – 1606Combined sources
Turni161 – 1644Combined sources
Beta strandi165 – 1717Combined sources
Beta strandi178 – 1814Combined sources
Beta strandi185 – 1917Combined sources
Beta strandi196 – 2005Combined sources
Turni201 – 2033Combined sources
Beta strandi206 – 2105Combined sources
Beta strandi217 – 22610Combined sources
Beta strandi229 – 23911Combined sources
Beta strandi242 – 2509Combined sources
Beta strandi253 – 26513Combined sources
Beta strandi269 – 2746Combined sources
Beta strandi280 – 2856Combined sources
Beta strandi290 – 2945Combined sources
Turni295 – 2984Combined sources
Beta strandi299 – 3046Combined sources
Beta strandi307 – 3104Combined sources
Beta strandi312 – 3176Combined sources
Beta strandi323 – 3286Combined sources
Beta strandi331 – 3377Combined sources
Turni340 – 3434Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4H5IX-ray1.36A/B1-354[»]
4H5JX-ray2.60A/B1-354[»]
ProteinModelPortaliP11655.
SMRiP11655. Positions 1-347.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati259 – 30042WD 1Add
BLAST
Repeati302 – 34140WD 2Add
BLAST

Sequence similaritiesi

Belongs to the WD repeat SEC12 family.Curated
Contains 2 WD repeats.Curated

Keywords - Domaini

Repeat, Signal-anchor, Transmembrane, Transmembrane helix, WD repeat

Phylogenomic databases

GeneTreeiENSGT00690000103233.
HOGENOMiHOG000000861.
InParanoidiP11655.
KOiK14003.
OMAiNEDETMA.
OrthoDBiEOG7CRV0N.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
InterProiIPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
[Graphical view]
SMARTiSM00320. WD40. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P11655-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFVTASYNV GYPAYGAKFL NNDTLLVAGG GGEGNNGIPN KLTVLRVDPT
60 70 80 90 100
KDTEKEQFHI LSEFALEDND DSPTAIDASK GIILVGCNEN STKITQGKGN
110 120 130 140 150
KHLRKFKYDK VNDQLEFLTS VDFDASTNAD DYTKLVYISR EGTVAAIASS
160 170 180 190 200
KVPAIMRIID PSDLTEKFEI ETRGEVKDLH FSTDGKVVAY ITGSSLEVIS
210 220 230 240 250
TVTGSCIARK TDFDKNWSLS KINFIADDTV LIAASLKKGK GIVLTKISIK
260 270 280 290 300
SGNTSVLRSK QVTNRFKGIT SMDVDMKGEL AVLASNDNSI ALVKLKDLSM
310 320 330 340 350
SKIFKQAHSF AITEVTISPD STYVASVSAA NTIHIIKLPL NYANYTSMKQ
360 370 380 390 400
KISKFFTNFI LIVLLSYILQ FSYKHNLHSM LFNYAKDNFL TKRDTISSPY
410 420 430 440 450
VVDEDLHQTT LFGNHGTKTS VPSVDSIKVH GVHETSSVNG TEVLCTESNI
460 470
INTGGAEFEI TNATFREIDD A
Length:471
Mass (Da):51,608
Last modified:October 1, 1989 - v1
Checksum:iDD4CEED041E776C3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X13161 Genomic DNA. Translation: CAA31559.1.
Z71641 Genomic DNA. Translation: CAA96306.1.
BK006947 Genomic DNA. Translation: DAA10566.1.
PIRiA31103.
RefSeqiNP_014423.1. NM_001183203.1.

Genome annotation databases

EnsemblFungiiYNR026C; YNR026C; YNR026C.
GeneIDi855760.
KEGGisce:YNR026C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X13161 Genomic DNA. Translation: CAA31559.1.
Z71641 Genomic DNA. Translation: CAA96306.1.
BK006947 Genomic DNA. Translation: DAA10566.1.
PIRiA31103.
RefSeqiNP_014423.1. NM_001183203.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4H5IX-ray1.36A/B1-354[»]
4H5JX-ray2.60A/B1-354[»]
ProteinModelPortaliP11655.
SMRiP11655. Positions 1-347.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35850. 53 interactions.
DIPiDIP-7541N.
IntActiP11655. 2 interactions.
MINTiMINT-1356711.

Proteomic databases

MaxQBiP11655.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNR026C; YNR026C; YNR026C.
GeneIDi855760.
KEGGisce:YNR026C.

Organism-specific databases

EuPathDBiFungiDB:YNR026C.
SGDiS000005309. SEC12.

Phylogenomic databases

GeneTreeiENSGT00690000103233.
HOGENOMiHOG000000861.
InParanoidiP11655.
KOiK14003.
OMAiNEDETMA.
OrthoDBiEOG7CRV0N.

Enzyme and pathway databases

BioCyciYEAST:G3O-33339-MONOMER.

Miscellaneous databases

PROiP11655.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
InterProiIPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
[Graphical view]
SMARTiSM00320. WD40. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A membrane glycoprotein, Sec12p, required for protein transport from the endoplasmic reticulum to the Golgi apparatus in yeast."
    Nakano A., Brada D., Schekman R.W.
    J. Cell Biol. 107:851-863(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
  2. "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.
    , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
    Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "Identification of 23 complementation groups required for post-translational events in the yeast secretory pathway."
    Novick P., Field C., Schekman R.W.
    Cell 21:205-215(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "A novel GTP-binding protein, Sar1p, is involved in transport from the endoplasmic reticulum to the Golgi apparatus."
    Nakano A., Muramatsu M.-A.
    J. Cell Biol. 109:2677-2691(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "Distinct biochemical requirements for the budding, targeting, and fusion of ER-derived transport vesicles."
    Rexach M.F., Schekman R.W.
    J. Cell Biol. 114:219-229(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Sec12p-dependent membrane binding of the small GTP-binding protein Sar1p promotes formation of transport vesicles from the ER."
    d'Enfert C., Wuestehube L.J., Lila T., Schekman R.W.
    J. Cell Biol. 114:663-670(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Reconstitution of GTP-binding Sar1 protein function in ER to Golgi transport."
    Oka T., Nishikawa S., Nakano A.
    J. Cell Biol. 114:671-679(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "Structural and functional dissection of a membrane glycoprotein required for vesicle budding from the endoplasmic reticulum."
    d'Enfert C., Barlowe C., Nishikawa S., Nakano A., Schekman R.W.
    Mol. Cell. Biol. 11:5727-5734(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TOPOLOGY, GLYCOSYLATION.
  10. "Genes that allow yeast cells to grow in the absence of the HDEL receptor."
    Hardwick K.G., Boothroyd J.C., Rudner A.D., Pelham H.R.B.
    EMBO J. 11:4187-4195(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  11. "SEC12 encodes a guanine-nucleotide-exchange factor essential for transport vesicle budding from the ER."
    Barlowe C., Schekman R.W.
    Nature 365:347-349(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  12. "Identification of a gene required for membrane protein retention in the early secretory pathway."
    Nishikawa S., Nakano A.
    Proc. Natl. Acad. Sci. U.S.A. 90:8179-8183(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  13. "Inhibition of GTP hydrolysis by Sar1p causes accumulation of vesicles that are a functional intermediate of the ER-to-Golgi transport in yeast."
    Oka T., Nakano A.
    J. Cell Biol. 124:425-434(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  14. "Inhibition of endoplasmic reticulum (ER)-to-Golgi transport induces relocalization of binding protein (BiP) within the ER to form the BiP bodies."
    Nishikawa S., Hirata A., Nakano A.
    Mol. Biol. Cell 5:1129-1143(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  15. "Expression, purification, and assay of Sec12p: a Sar1p-specific GDP dissociation stimulator."
    Barlowe C., Schekman R.W.
    Methods Enzymol. 257:98-106(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  16. "Membrane protein retrieval from the Golgi apparatus to the endoplasmic reticulum (ER): characterization of the RER1 gene product as a component involved in ER localization of Sec12p."
    Sato K., Nishikawa S., Nakano A.
    Mol. Biol. Cell 6:1459-1477(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  17. "Endoplasmic reticulum localization of Sec12p is achieved by two mechanisms: Rer1p-dependent retrieval that requires the transmembrane domain and Rer1p-independent retention that involves the cytoplasmic domain."
    Sato M., Sato K., Nakano A.
    J. Cell Biol. 134:279-293(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  18. "Sec12p requires Rer1p for sorting to coatomer (COPI)-coated vesicles and retrieval to the ER."
    Boehm J., Letourneur F., Ballensiefen W., Ossipov D., Demolliere C., Schmitt H.D.
    J. Cell Sci. 110:991-1003(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  19. "Selective packaging of cargo molecules into endoplasmic reticulum-derived COPII vesicles."
    Campbell J.L., Schekman R.W.
    Proc. Natl. Acad. Sci. U.S.A. 94:837-842(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  20. "Rer1p as common machinery for the endoplasmic reticulum localization of membrane proteins."
    Sato K., Sato M., Nakano A.
    Proc. Natl. Acad. Sci. U.S.A. 94:9693-9698(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  21. "Golgi structure correlates with transitional endoplasmic reticulum organization in Pichia pastoris and Saccharomyces cerevisiae."
    Rossanese O.W., Soderholm J., Bevis B.J., Sears I.B., O'Connor J., Williamson E.K., Glick B.S.
    J. Cell Biol. 145:69-81(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  22. "Autophagosome requires specific early Sec proteins for its formation and NSF/SNARE for vacuolar fusion."
    Ishihara N., Hamasaki M., Yokota S., Suzuki K., Kamada Y., Kihara A., Yoshimori T., Noda T., Ohsumi Y.
    Mol. Biol. Cell 12:3690-3702(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  23. "The yeast Sar exchange factor Sec12, and its higher organism orthologs, fold as beta-propellers."
    Chardin P., Callebaut I.
    FEBS Lett. 525:171-173(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: DOMAIN.
  24. "The early secretory pathway contributes to autophagy in yeast."
    Hamasaki M., Noda T., Ohsumi Y.
    Cell Struct. Funct. 28:49-54(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  25. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  26. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  27. "Purification and functional properties of yeast Sec12 GEF."
    Futai E., Schekman R.W.
    Methods Enzymol. 404:74-82(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiSEC12_YEAST
AccessioniPrimary (citable) accession number: P11655
Secondary accession number(s): D6W1K0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: July 6, 2016
This is version 143 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

In the process of transport, SEC12 itself may migrate to the Golgi apparatus and function in subsequent transport events.
Present with 6160 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.