AP3D_YEAST
ID AP3D_YEAST Reviewed; 932 AA.
AC Q08951; D6W3H3; Q02737; Q7LIB1;
DT 21-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 169.
DE RecName: Full=AP-3 complex subunit delta;
DE AltName: Full=Adaptor-related protein complex 3 subunit delta;
DE AltName: Full=Delta-adaptin 3;
DE Short=Delta-adaptin;
GN Name=APL5; Synonyms=YKS4; OrderedLocusNames=YPL195W;
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=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
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] OF 8-932.
RA Robinson L.C., Engle H.M., Panek H.R.;
RT "Suppressors of loss of yeast casein kinase 1 function define the four
RT subunits of a novel putative adaptin complex.";
RL Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP IDENTIFICATION OF THE AP-3 COMPLEX, AND FUNCTION OF THE AP-3 COMPLEX.
RX PubMed=9335339; DOI=10.1016/s0092-8674(01)80013-1;
RA Cowles C.R., Odorizzi G., Payne G.S., Emr S.D.;
RT "The AP-3 adaptor complex is essential for cargo-selective transport to the
RT yeast vacuole.";
RL Cell 91:109-118(1997).
RN [5]
RP IDENTIFICATION OF THE AP-3 COMPLEX, AND FUNCTION OF THE AP-3 COMPLEX.
RX PubMed=9250663; DOI=10.1093/emboj/16.14.4194;
RA Panek H.R., Stepp J.D., Engle H.M., Marks K.M., Tan P.K., Lemmon S.K.,
RA Robinson L.C.;
RT "Suppressors of YCK-encoded yeast casein kinase 1 deficiency define the
RT four subunits of a novel clathrin AP-like complex.";
RL EMBO J. 16:4194-4204(1997).
RN [6]
RP SUBCELLULAR LOCATION, INTERACTION WITH VPS41, AND FUNCTION OF THE AP-3
RP COMPLEX.
RX PubMed=10559961; DOI=10.1038/14037;
RA Rehling P., Darsow T., Katzmann D.J., Emr S.D.;
RT "Formation of AP-3 transport intermediates requires Vps41 function.";
RL Nat. Cell Biol. 1:346-353(1999).
RN [7]
RP INTERACTION WITH VPS41.
RX PubMed=11160821; DOI=10.1091/mbc.12.1.37;
RA Darsow T., Katzmann D.J., Cowles C.R., Emr S.D.;
RT "Vps41p function in the alkaline phosphatase pathway requires homo-
RT oligomerization and interaction with AP-3 through two distinct domains.";
RL Mol. Biol. Cell 12:37-51(2001).
RN [8]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [9]
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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-767; SER-888 AND SER-918, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-727; SER-798 AND SER-918, AND
RP IDENTIFICATION BY 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).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-700; THR-767; SER-770;
RP SER-773; SER-798; SER-888 AND SER-918, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [13]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT THR-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: Part of the AP-3 complex, an adaptor-related complex which is
CC not clathrin-associated. The complex is associated with the Golgi
CC region as well as more peripheral structures. It facilitates the
CC budding of vesicles from the Golgi membrane and may be directly
CC involved in trafficking to the vacuole. Required for the transport via
CC the ALP pathway, which directs the transport of the cargo proteins PHO8
CC and VAM3 to the vacuole. {ECO:0000269|PubMed:10559961,
CC ECO:0000269|PubMed:9250663, ECO:0000269|PubMed:9335339}.
CC -!- SUBUNIT: Adaptor protein complex 3 (AP-3) is a heterotetramer composed
CC of 2 large adaptins (APL5 and APL6), a medium adaptin (APM3) and a
CC small adaptin (APS3). Interacts with VPS41.
CC {ECO:0000269|PubMed:10559961, ECO:0000269|PubMed:11160821}.
CC -!- INTERACTION:
CC Q08951; P46682: APL6; NbExp=5; IntAct=EBI-29702, EBI-2213;
CC Q08951; P38153: APM3; NbExp=4; IntAct=EBI-29702, EBI-2710;
CC -!- SUBCELLULAR LOCATION: Golgi apparatus {ECO:0000269|PubMed:10559961,
CC ECO:0000269|PubMed:14562095}. Cytoplasmic vesicle, clathrin-coated
CC vesicle membrane {ECO:0000269|PubMed:10559961}; Peripheral membrane
CC protein {ECO:0000305|PubMed:10559961}; Cytoplasmic side
CC {ECO:0000305|PubMed:10559961}. Note=Component of the coat surrounding
CC the cytoplasmic face of coated vesicles located at the Golgi complex.
CC {ECO:0000269|PubMed:10559961}.
CC -!- MISCELLANEOUS: Present with 13500 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the adaptor complexes large subunit family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA79850.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; Z73551; CAA97908.1; -; Genomic_DNA.
DR EMBL; U36858; AAA79850.1; ALT_FRAME; Genomic_DNA.
DR EMBL; BK006949; DAA11239.1; -; Genomic_DNA.
DR PIR; S65214; S65214.
DR RefSeq; NP_015129.1; NM_001184009.1.
DR PDB; 7P3X; EM; 9.10 A; A=1-932.
DR PDB; 7P3Y; EM; 10.10 A; A=1-932.
DR PDB; 7P3Z; EM; 10.50 A; A=1-932.
DR PDBsum; 7P3X; -.
DR PDBsum; 7P3Y; -.
DR PDBsum; 7P3Z; -.
DR AlphaFoldDB; Q08951; -.
DR SMR; Q08951; -.
DR BioGRID; 35988; 176.
DR ComplexPortal; CPX-535; Adapter complex AP-3.
DR DIP; DIP-3977N; -.
DR IntAct; Q08951; 7.
DR MINT; Q08951; -.
DR STRING; 4932.YPL195W; -.
DR iPTMnet; Q08951; -.
DR MaxQB; Q08951; -.
DR PaxDb; Q08951; -.
DR PRIDE; Q08951; -.
DR EnsemblFungi; YPL195W_mRNA; YPL195W; YPL195W.
DR GeneID; 855906; -.
DR KEGG; sce:YPL195W; -.
DR SGD; S000006116; APL5.
DR VEuPathDB; FungiDB:YPL195W; -.
DR eggNOG; KOG1059; Eukaryota.
DR GeneTree; ENSGT00550000075067; -.
DR HOGENOM; CLU_001908_1_1_1; -.
DR InParanoid; Q08951; -.
DR OMA; YYAAAWI; -.
DR BioCyc; YEAST:G3O-34088-MON; -.
DR PRO; PR:Q08951; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q08951; protein.
DR GO; GO:0030123; C:AP-3 adaptor complex; IMP:SGD.
DR GO; GO:0030665; C:clathrin-coated vesicle membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0010008; C:endosome membrane; IBA:GO_Central.
DR GO; GO:0005794; C:Golgi apparatus; IEA:UniProtKB-SubCell.
DR GO; GO:0006896; P:Golgi to vacuole transport; IMP:SGD.
DR GO; GO:0006886; P:intracellular protein transport; IC:ComplexPortal.
DR GO; GO:0006623; P:protein targeting to vacuole; IMP:SGD.
DR Gene3D; 1.25.10.10; -; 1.
DR InterPro; IPR017105; AP3_complex_dsu.
DR InterPro; IPR011989; ARM-like.
DR InterPro; IPR016024; ARM-type_fold.
DR InterPro; IPR002553; Clathrin/coatomer_adapt-like_N.
DR PANTHER; PTHR22781; PTHR22781; 1.
DR Pfam; PF01602; Adaptin_N; 1.
DR PIRSF; PIRSF037092; AP3_complex_delta; 1.
DR SUPFAM; SSF48371; SSF48371; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Coiled coil; Cytoplasmic vesicle;
KW Golgi apparatus; Membrane; Phosphoprotein; Protein transport;
KW Reference proteome; Repeat; Transport.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CHAIN 2..932
FT /note="AP-3 complex subunit delta"
FT /id="PRO_0000227676"
FT REPEAT 157..194
FT /note="HEAT 1"
FT REPEAT 196..231
FT /note="HEAT 2"
FT REPEAT 233..269
FT /note="HEAT 3"
FT REPEAT 270..307
FT /note="HEAT 4"
FT REPEAT 310..346
FT /note="HEAT 5"
FT REPEAT 347..384
FT /note="HEAT 6"
FT REPEAT 386..425
FT /note="HEAT 7"
FT REPEAT 427..466
FT /note="HEAT 8"
FT REPEAT 490..527
FT /note="HEAT 9"
FT REPEAT 528..564
FT /note="HEAT 10"
FT REPEAT 570..601
FT /note="HEAT 11"
FT REPEAT 602..638
FT /note="HEAT 12"
FT REGION 720..868
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 897..932
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 858..878
FT /evidence="ECO:0000255"
FT COMPBIAS 720..764
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 765..779
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 793..836
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 838..858
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 913..932
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylthreonine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES 700
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 727
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 767
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 770
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 773
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 798
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 888
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 918
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
SQ SEQUENCE 932 AA; 106924 MW; 51415466FF25CC40 CRC64;
MTSLYAPGAE DIRQRLRPFG FFFEKSLKDL IKGIRSHNET PEKLDQFFKQ VLSECREEVN
SPDLNSKTNA VLKLTYLEMY GFDMAWCNFH ILEVMSSNKL QQKRVGYLAA SQSFYKDSDI
LMLATNLLKK DLKYDGNNDV VKVGIALSGL STIITPSLAR DIADDLFTML NSTRPYIRKK
AITALFKVFL QYPEALRDNF DKFVSKLDDD DISVVSAAVS VICELSKKNP QPFIQLSPLL
YEILVTIDNN WIIIRLLKLF TNLSQVEPKL RAKLLPKILE LMESTVATSV IYESVNCIVK
GNMLEEDDFE TAMACLERLH TFCDSQDPNL RYISCILFYK IGKINTDFIS RFDQLIIRLL
SDVDVSIRSK AIELVEGIVD EDNLKAIVQT LMKQFVDEDV VILQTGSIVY EKSKRIPIII
PENYKIKMVN VIISICSADN YSSVNDFEWY NAVIMDLAML CQDISDKSLG SKIGEQFRNL
MIKVPSMREV TIANIIKLIS NDNINKQLPT VLRECIWCLG EFSTLVENGN DLIKIMTENI
SYYSHSVQEV LILALVKVFS NWCNNFQEDK RFEIKMVLKE LIEFFENLSY SSTFEVQERS
VEVLEFLRLS LEALEEDTEG LPMLLSEVLP SFFNAYELAP IARGTQLKLA VDENLDLETP
FLTKEAADEL LDEQKSDAIS DLMSDISMDE QVELKFVDDS DTSYEEKEKL DDFENPFEIE
REKERMSNPY YLGEEDEERT KNSKDLLDLN EEESSDKKPE TIRLNRTDNS LNSLSLSTTE
ISRKKKKGKK KNRVQVLSDE PVIEAAPKRK DAFQKPHDNH STQNPLKKDK INLRMHSQLE
NFDFSNFGQS SNAGRGSQEE GNLRKEDELE LSRLEANLIV KDEKDNLSDT EEVIVIKKKK
KGKKSKSKNK LKTKAKNSPE PNEFLRDQST DI
