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Coatomer subunit delta (Delta-coat protein) (Delta-COP)

 COPD_YEAST              Reviewed;         546 AA.
P43621; D6VTT4;
01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
22-NOV-2017, entry version 165.
RecName: Full=Coatomer subunit delta;
AltName: Full=Delta-coat protein;
Short=Delta-COP;
Name=RET2; OrderedLocusNames=YFR051C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=7670463; DOI=10.1038/ng0795-261;
Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M.,
Sasanuma S., Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K.,
Yamazaki M., Tashiro H., Eki T.;
"Analysis of the nucleotide sequence of chromosome VI from
Saccharomyces cerevisiae.";
Nat. Genet. 10:261-268(1995).
[2]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204511 / S288c / AB972;
PubMed=8686379;
DOI=10.1002/(SICI)1097-0061(199602)12:2<149::AID-YEA893>3.0.CO;2-G;
Eki T., Naitou M., Hagiwara H., Ozawa M., Sasanuma S., Sasanuma M.,
Tsuchiya Y., Shibata T., Hanaoka F., Murakami Y.;
"Analysis of a 36.2 kb DNA sequence including the right telomere of
chromosome VI from Saccharomyces cerevisiae.";
Yeast 12:149-167(1996).
[4]
PROTEIN SEQUENCE OF 2-15, AND CHARACTERIZATION.
PubMed=8617224;
Cosson P., Demolliere C., Hennecke S., Duden R., Letourneur F.;
"Delta- and zeta-COP, two coatomer subunits homologous to clathrin-
associated proteins, are involved in ER retrieval.";
EMBO J. 15:1792-1798(1996).
[5]
INTERACTION WITH DSL1.
PubMed=14504276; DOI=10.1074/jbc.M308740200;
Andag U., Schmitt H.D.;
"Dsl1p, an essential component of the Golgi-endoplasmic reticulum
retrieval system in yeast, uses the same sequence motif to interact
with different subunits of the COPI vesicle coat.";
J. Biol. Chem. 278:51722-51734(2003).
[6]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[7]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-277, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
-!- FUNCTION: The coatomer is a cytosolic protein complex that binds
to dilysine motifs and reversibly associates with Golgi non-
clathrin-coated vesicles, which further mediate biosynthetic
protein transport from the ER, via the Golgi up to the trans Golgi
network. Coatomer complex is required for budding from Golgi
membranes, and is essential for the retrograde Golgi-to-ER
transport of dilysine-tagged proteins (By similarity).
{ECO:0000250}.
-!- SUBUNIT: Oligomeric complex that consists of at least the alpha,
beta, beta', gamma, delta, epsilon and zeta subunits. Interacts
with DSL1. {ECO:0000269|PubMed:14504276}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Golgi apparatus
membrane {ECO:0000250}; Peripheral membrane protein {ECO:0000250};
Cytoplasmic side {ECO:0000250}. Cytoplasmic vesicle, COPI-coated
vesicle membrane {ECO:0000250}; Peripheral membrane protein
{ECO:0000250}; Cytoplasmic side {ECO:0000250}. Note=The coatomer
is cytoplasmic or polymerized on the cytoplasmic side of the
Golgi, as well as on the vesicles/buds originating from it.
{ECO:0000250}.
-!- MISCELLANEOUS: Present with 18000 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the adaptor complexes medium subunit
family. Delta-COP subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; D50617; BAA09290.1; -; Genomic_DNA.
EMBL; BK006940; DAA12494.1; -; Genomic_DNA.
PIR; S56306; S56306.
RefSeq; NP_116709.3; NM_001180016.3.
PDB; 5FJW; X-ray; 2.80 A; A/B/C/D/E/F/G/H=288-546.
PDB; 5FJX; X-ray; 2.45 A; A/B/C=282-546.
PDB; 5FJZ; X-ray; 1.90 A; A/B/C/D=282-546.
PDB; 5FK0; X-ray; 3.00 A; A/B/C/D/E/F/G/H=282-546.
PDBsum; 5FJW; -.
PDBsum; 5FJX; -.
PDBsum; 5FJZ; -.
PDBsum; 5FK0; -.
ProteinModelPortal; P43621; -.
SMR; P43621; -.
BioGrid; 31209; 355.
DIP; DIP-5255N; -.
IntAct; P43621; 38.
MINT; MINT-548122; -.
STRING; 4932.YFR051C; -.
iPTMnet; P43621; -.
MaxQB; P43621; -.
PRIDE; P43621; -.
EnsemblFungi; YFR051C; YFR051C; YFR051C.
GeneID; 850612; -.
KEGG; sce:YFR051C; -.
EuPathDB; FungiDB:YFR051C; -.
SGD; S000001947; RET2.
GeneTree; ENSGT00390000017207; -.
HOGENOM; HOG000203984; -.
InParanoid; P43621; -.
KO; K20471; -.
OMA; KTFVEMD; -.
OrthoDB; EOG092C50I9; -.
BioCyc; YEAST:G3O-30497-MONOMER; -.
Reactome; R-SCE-6807878; COPI-mediated anterograde transport.
Reactome; R-SCE-6811434; COPI-dependent Golgi-to-ER retrograde traffic.
PRO; PR:P43621; -.
Proteomes; UP000002311; Chromosome VI.
GO; GO:0030126; C:COPI vesicle coat; IMP:SGD.
GO; GO:0000139; C:Golgi membrane; IEA:UniProtKB-SubCell.
GO; GO:0006888; P:ER to Golgi vesicle-mediated transport; IMP:SGD.
GO; GO:0048313; P:Golgi inheritance; IGI:SGD.
GO; GO:0051645; P:Golgi localization; IGI:SGD.
GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
GO; GO:0006890; P:retrograde vesicle-mediated transport, Golgi to ER; IMP:SGD.
InterPro; IPR036168; AP2_Mu_C_sf.
InterPro; IPR022775; AP_mu_sigma_su.
InterPro; IPR027059; Coatomer_dsu.
InterPro; IPR011012; Longin-like_dom_sf.
InterPro; IPR028565; MHD.
PANTHER; PTHR10121; PTHR10121; 1.
Pfam; PF01217; Clat_adaptor_s; 1.
SUPFAM; SSF49447; SSF49447; 1.
SUPFAM; SSF64356; SSF64356; 1.
PROSITE; PS51072; MHD; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Cytoplasmic vesicle;
Direct protein sequencing; ER-Golgi transport; Golgi apparatus;
Membrane; Phosphoprotein; Protein transport; Reference proteome;
Transport.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:8617224}.
CHAIN 2 546 Coatomer subunit delta.
/FTId=PRO_0000193848.
DOMAIN 288 546 MHD. {ECO:0000255|PROSITE-
ProRule:PRU00404}.
REGION 190 440 Interaction with DSL1.
{ECO:0000269|PubMed:14504276}.
MOD_RES 277 277 Phosphothreonine.
{ECO:0000244|PubMed:18407956}.
STRAND 289 303 {ECO:0000244|PDB:5FJZ}.
STRAND 309 322 {ECO:0000244|PDB:5FJZ}.
HELIX 325 327 {ECO:0000244|PDB:5FJZ}.
STRAND 328 334 {ECO:0000244|PDB:5FJZ}.
HELIX 343 345 {ECO:0000244|PDB:5FJZ}.
HELIX 355 361 {ECO:0000244|PDB:5FJZ}.
STRAND 362 364 {ECO:0000244|PDB:5FJZ}.
STRAND 366 368 {ECO:0000244|PDB:5FJZ}.
STRAND 380 389 {ECO:0000244|PDB:5FJZ}.
STRAND 398 407 {ECO:0000244|PDB:5FJZ}.
STRAND 409 422 {ECO:0000244|PDB:5FJZ}.
STRAND 428 436 {ECO:0000244|PDB:5FJZ}.
HELIX 447 449 {ECO:0000244|PDB:5FJZ}.
TURN 451 454 {ECO:0000244|PDB:5FJX}.
STRAND 456 458 {ECO:0000244|PDB:5FJZ}.
STRAND 463 473 {ECO:0000244|PDB:5FJZ}.
STRAND 478 486 {ECO:0000244|PDB:5FJZ}.
HELIX 490 493 {ECO:0000244|PDB:5FJZ}.
STRAND 495 499 {ECO:0000244|PDB:5FJZ}.
STRAND 501 505 {ECO:0000244|PDB:5FJZ}.
STRAND 517 524 {ECO:0000244|PDB:5FJZ}.
STRAND 525 529 {ECO:0000244|PDB:5FJX}.
STRAND 533 545 {ECO:0000244|PDB:5FJZ}.
SEQUENCE 546 AA; 60628 MW; AA730F046655EE5A CRC64;
MVVLAASITT RQGKPLLSRQ FKDLSKDRVL ELLSNFQNLV SEISSDHTFV EDKHVRYVYR
PFDNYYIILI TNRQSNIIKD LATLNLFSQT INSYLSSFQD QEIFHNAFEI LSSFDEIVSM
GGYKENLSFT QVQTYLSMES HEERIQEIIE RNKEIEATEE RKRRAKEIAR KEHERKHGFM
SSNGDYDGAN RFMGSKDPNV TNAINSYYSH ASPAAQQSYL QSSHAAAAEV APVASPMATS
QRAGHSATGG MKLGGGAGRR AGAAPRPSAI SSASSGTPPP PEEDVPENNG ILISIKEVIN
AEFSRDGTIH SSELKGVLEL RINDHDLSHS NLKLADSIDV RDKSFQFKTH PNIDKQSFLS
TKLISLRDKS KAFPANDQSL GVLRWRKVAP AEDDSLIPLT LTTWVSPSES QQGFDVIIEY
ESVLETELAD VIFTIPVFPQ EPVDINTESS TCSDAEVVNM DQEMGTSIKI SKIAANDAGA
LAFTIEAPYE DALYPMTVSF QESTRDKLAK SFTGMAIQSV VMANDHDQEL PYDVITSLKS
DEYLVQ


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