COPD_YEAST
ID COPD_YEAST Reviewed; 546 AA.
AC P43621; D6VTT4;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 193.
DE RecName: Full=Coatomer subunit delta;
DE AltName: Full=Delta-coat protein;
DE Short=Delta-COP;
GN Name=RET2; OrderedLocusNames=YFR051C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7670463; DOI=10.1038/ng0795-261;
RA Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S.,
RA Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K., Yamazaki M., Tashiro H.,
RA Eki T.;
RT "Analysis of the nucleotide sequence of chromosome VI from Saccharomyces
RT cerevisiae.";
RL Nat. Genet. 10:261-268(1995).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204511 / S288c / AB972;
RX PubMed=8686379;
RX DOI=10.1002/(sici)1097-0061(199602)12:2<149::aid-yea893>3.0.co;2-g;
RA Eki T., Naitou M., Hagiwara H., Ozawa M., Sasanuma S., Sasanuma M.,
RA Tsuchiya Y., Shibata T., Hanaoka F., Murakami Y.;
RT "Analysis of a 36.2 kb DNA sequence including the right telomere of
RT chromosome VI from Saccharomyces cerevisiae.";
RL Yeast 12:149-167(1996).
RN [4]
RP PROTEIN SEQUENCE OF 2-15, AND CHARACTERIZATION.
RX PubMed=8617224; DOI=10.1002/j.1460-2075.1996.tb00528.x;
RA Cosson P., Demolliere C., Hennecke S., Duden R., Letourneur F.;
RT "Delta- and zeta-COP, two coatomer subunits homologous to clathrin-
RT associated proteins, are involved in ER retrieval.";
RL EMBO J. 15:1792-1798(1996).
RN [5]
RP INTERACTION WITH DSL1.
RX PubMed=14504276; DOI=10.1074/jbc.m308740200;
RA Andag U., Schmitt H.D.;
RT "Dsl1p, an essential component of the Golgi-endoplasmic reticulum retrieval
RT system in yeast, uses the same sequence motif to interact with different
RT subunits of the COPI vesicle coat.";
RL J. Biol. Chem. 278:51722-51734(2003).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-277, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
CC -!- FUNCTION: The coatomer is a cytosolic protein complex that binds to
CC dilysine motifs and reversibly associates with Golgi non-clathrin-
CC coated vesicles, which further mediate biosynthetic protein transport
CC from the ER, via the Golgi up to the trans Golgi network. Coatomer
CC complex is required for budding from Golgi membranes, and is essential
CC for the retrograde Golgi-to-ER transport of dilysine-tagged proteins
CC (By similarity). {ECO:0000250}.
CC -!- SUBUNIT: Oligomeric complex that consists of at least the alpha, beta,
CC beta', gamma, delta, epsilon and zeta subunits. Interacts with DSL1.
CC {ECO:0000269|PubMed:14504276}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Golgi apparatus membrane
CC {ECO:0000250}; Peripheral membrane protein {ECO:0000250}; Cytoplasmic
CC side {ECO:0000250}. Cytoplasmic vesicle, COPI-coated vesicle membrane
CC {ECO:0000250}; Peripheral membrane protein {ECO:0000250}; Cytoplasmic
CC side {ECO:0000250}. Note=The coatomer is cytoplasmic or polymerized on
CC the cytoplasmic side of the Golgi, as well as on the vesicles/buds
CC originating from it. {ECO:0000250}.
CC -!- MISCELLANEOUS: Present with 18000 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the adaptor complexes medium subunit family.
CC Delta-COP subfamily. {ECO:0000305}.
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DR EMBL; D50617; BAA09290.1; -; Genomic_DNA.
DR EMBL; BK006940; DAA12494.1; -; Genomic_DNA.
DR PIR; S56306; S56306.
DR RefSeq; NP_116709.3; NM_001180016.3.
DR PDB; 5FJW; X-ray; 2.80 A; A/B/C/D/E/F/G/H=288-546.
DR PDB; 5FJX; X-ray; 2.45 A; A/B/C=282-546.
DR PDB; 5FJZ; X-ray; 1.90 A; A/B/C/D=282-546.
DR PDB; 5FK0; X-ray; 3.00 A; A/B/C/D/E/F/G/H=282-546.
DR PDBsum; 5FJW; -.
DR PDBsum; 5FJX; -.
DR PDBsum; 5FJZ; -.
DR PDBsum; 5FK0; -.
DR AlphaFoldDB; P43621; -.
DR SMR; P43621; -.
DR BioGRID; 31209; 512.
DR ComplexPortal; CPX-1652; COPI vesicle coat complex.
DR DIP; DIP-5255N; -.
DR IntAct; P43621; 40.
DR MINT; P43621; -.
DR STRING; 4932.YFR051C; -.
DR iPTMnet; P43621; -.
DR MaxQB; P43621; -.
DR PaxDb; P43621; -.
DR PRIDE; P43621; -.
DR EnsemblFungi; YFR051C_mRNA; YFR051C; YFR051C.
DR GeneID; 850612; -.
DR KEGG; sce:YFR051C; -.
DR SGD; S000001947; RET2.
DR VEuPathDB; FungiDB:YFR051C; -.
DR eggNOG; KOG2635; Eukaryota.
DR GeneTree; ENSGT00390000017207; -.
DR HOGENOM; CLU_019988_3_0_1; -.
DR InParanoid; P43621; -.
DR OMA; YDARKHV; -.
DR BioCyc; YEAST:G3O-30497-MON; -.
DR Reactome; R-SCE-6807878; COPI-mediated anterograde transport.
DR Reactome; R-SCE-6811434; COPI-dependent Golgi-to-ER retrograde traffic.
DR PRO; PR:P43621; -.
DR Proteomes; UP000002311; Chromosome VI.
DR RNAct; P43621; protein.
DR GO; GO:0030126; C:COPI vesicle coat; IDA:SGD.
DR GO; GO:0000139; C:Golgi membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0006888; P:endoplasmic reticulum to Golgi vesicle-mediated transport; IMP:SGD.
DR GO; GO:0051645; P:Golgi localization; IBA:GO_Central.
DR GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR GO; GO:0006890; P:retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum; IMP:SGD.
DR InterPro; IPR036168; AP2_Mu_C_sf.
DR InterPro; IPR022775; AP_mu_sigma_su.
DR InterPro; IPR027059; Coatomer_dsu.
DR InterPro; IPR011012; Longin-like_dom_sf.
DR InterPro; IPR028565; MHD.
DR PANTHER; PTHR10121; PTHR10121; 1.
DR Pfam; PF01217; Clat_adaptor_s; 1.
DR SUPFAM; SSF49447; SSF49447; 1.
DR SUPFAM; SSF64356; SSF64356; 1.
DR PROSITE; PS51072; MHD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Cytoplasmic vesicle; Direct protein sequencing;
KW ER-Golgi transport; Golgi apparatus; Membrane; Phosphoprotein;
KW Protein transport; Reference proteome; Transport.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8617224"
FT CHAIN 2..546
FT /note="Coatomer subunit delta"
FT /id="PRO_0000193848"
FT DOMAIN 288..546
FT /note="MHD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00404"
FT REGION 190..440
FT /note="Interaction with DSL1"
FT /evidence="ECO:0000269|PubMed:14504276"
FT REGION 236..287
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 277
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT STRAND 289..303
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 309..322
FT /evidence="ECO:0007829|PDB:5FJZ"
FT HELIX 325..327
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 328..334
FT /evidence="ECO:0007829|PDB:5FJZ"
FT HELIX 343..345
FT /evidence="ECO:0007829|PDB:5FJZ"
FT HELIX 355..361
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 362..364
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 366..368
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 380..389
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 398..407
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 409..422
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 428..436
FT /evidence="ECO:0007829|PDB:5FJZ"
FT HELIX 447..449
FT /evidence="ECO:0007829|PDB:5FJZ"
FT TURN 451..454
FT /evidence="ECO:0007829|PDB:5FJX"
FT STRAND 456..458
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 463..473
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 478..486
FT /evidence="ECO:0007829|PDB:5FJZ"
FT HELIX 490..493
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 495..499
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 501..505
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 517..524
FT /evidence="ECO:0007829|PDB:5FJZ"
FT STRAND 525..529
FT /evidence="ECO:0007829|PDB:5FJX"
FT STRAND 533..545
FT /evidence="ECO:0007829|PDB:5FJZ"
SQ 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
