VPS28_YEAST
ID VPS28_YEAST Reviewed; 242 AA.
AC Q02767; D6W3V0; E9P8X2; P87328;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 181.
DE RecName: Full=Vacuolar protein sorting-associated protein 28;
DE AltName: Full=ESCRT-I complex subunit VPS28;
GN Name=VPS28; Synonyms=VPT28; OrderedLocusNames=YPL065W; ORFNames=LPE5W;
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 [GENOMIC DNA].
RX PubMed=8817003; DOI=10.1091/mbc.7.6.985;
RA Rieder S.E., Banta L.M., Koehrer K., McCaffery J.M., Emr S.D.;
RT "Multilamellar endosome-like compartment accumulates in the yeast vps28
RT vacuolar protein sorting mutant.";
RL Mol. Biol. Cell 7:985-999(1996).
RN [2]
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
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 [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 SUBCELLULAR LOCATION, AND INTERACTION WITH VPS27.
RX PubMed=12900393; DOI=10.1083/jcb.200302136;
RA Katzmann D.J., Stefan C.J., Babst M., Emr S.D.;
RT "Vps27 recruits ESCRT machinery to endosomes during MVB sorting.";
RL J. Cell Biol. 162:413-423(2003).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (3.6 ANGSTROMS) OF 1-147 IN COMPLEX WITH STP22 AND
RP SRN2, AND INTERACTION WITH VPS36.
RX PubMed=16615893; DOI=10.1016/j.cell.2006.01.047;
RA Teo H., Gill D.J., Sun J., Perisic O., Veprintsev D.B., Vallis Y.,
RA Emr S.D., Williams R.L.;
RT "ESCRT-I core and ESCRT-II GLUE domain structures reveal role for GLUE in
RT linking to ESCRT-I and membranes.";
RL Cell 125:99-111(2006).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 13-125 IN COMPLEX WITH STP22 AND
RP SRN2, AND MUTAGENESIS OF LEU-40 AND TYR-44.
RX PubMed=16615894; DOI=10.1016/j.cell.2006.01.049;
RA Kostelansky M.S., Sun J., Lee S., Kim J., Ghirlando R., Hierro A.,
RA Emr S.D., Hurley J.H.;
RT "Structural and functional organization of the ESCRT-I trafficking
RT complex.";
RL Cell 125:113-126(2006).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (3.05 ANGSTROMS) OF 148-241, SELF-ASSOCIATION,
RP INTERACTION WITH VPS20, AND MUTAGENESIS OF 228-PHE--GLU-231.
RX PubMed=16749904; DOI=10.1111/j.1600-0854.2006.00440.x;
RA Pineda-Molina E., Belrhali H., Piefer A.J., Akula I., Bates P.,
RA Weissenhorn W.;
RT "The crystal structure of the C-terminal domain of Vps28 reveals a
RT conserved surface required for Vps20 recruitment.";
RL Traffic 7:1007-1016(2006).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 148-242, AND COMPOSITION OF THE
RP ESCRT-I COMPLEX.
RX PubMed=17215868; DOI=10.1038/sj.emboj.7601501;
RA Gill D.J., Teo H., Sun J., Perisic O., Veprintsev D.B., Emr S.D.,
RA Williams R.L.;
RT "Structural insight into the ESCRT-I/-II link and its role in MVB
RT trafficking.";
RL EMBO J. 26:600-612(2007).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 1-118, AND COMPOSITION OF THE
RP ESCRT-I COMPLEX.
RX PubMed=17442384; DOI=10.1016/j.cell.2007.03.016;
RA Kostelansky M.S., Schluter C., Tam Y.Y., Lee S., Ghirlando R., Beach B.,
RA Conibear E., Hurley J.H.;
RT "Molecular architecture and functional model of the complete yeast ESCRT-I
RT heterotetramer.";
RL Cell 129:485-498(2007).
CC -!- FUNCTION: Component of the ESCRT-I complex, a regulator of vesicular
CC trafficking process. Required for normal endocytic and biosynthetic
CC traffic to the yeast vacuole.
CC -!- SUBUNIT: Component of the ESCRT-I complex (endosomal sorting complex
CC required for transport I) which consists of STP22, VPS28, SRN2 and
CC MVB12 in a 1:1:1:1 stoichiometry. Self-associates. Interacts with
CC VPS27; the interaction mediates the association with the ESCRT-0
CC complex. Interacts with VPS20; the interaction mediates the association
CC with the ESCRT-III complex. {ECO:0000269|PubMed:12900393,
CC ECO:0000269|PubMed:16615893, ECO:0000269|PubMed:16615894,
CC ECO:0000269|PubMed:16749904}.
CC -!- INTERACTION:
CC Q02767; Q99176: SRN2; NbExp=5; IntAct=EBI-20387, EBI-18076;
CC Q02767; P25604: STP22; NbExp=4; IntAct=EBI-20387, EBI-411625;
CC Q02767; Q06696: VPS36; NbExp=6; IntAct=EBI-20387, EBI-36540;
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Endosome. Late endosome membrane
CC {ECO:0000305}; Peripheral membrane protein {ECO:0000305}.
CC -!- MISCELLANEOUS: Present with 1420 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the VPS28 family. {ECO:0000255|PROSITE-
CC ProRule:PRU00642, ECO:0000255|PROSITE-ProRule:PRU00645}.
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DR EMBL; U50630; AAB40936.1; -; Genomic_DNA.
DR EMBL; U39205; AAB68300.1; -; Genomic_DNA.
DR EMBL; AY692790; AAT92809.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11366.1; -; Genomic_DNA.
DR PIR; S60925; S60925.
DR RefSeq; NP_015260.1; NM_001183879.1.
DR PDB; 2CAZ; X-ray; 3.60 A; B/E=1-147.
DR PDB; 2F66; X-ray; 2.80 A; B/E=13-125.
DR PDB; 2F6M; X-ray; 2.10 A; B/D=13-118.
DR PDB; 2G3K; X-ray; 3.05 A; A/B/C/D/E/F/G=148-241.
DR PDB; 2J9U; X-ray; 2.00 A; A/C=148-242.
DR PDB; 2J9V; X-ray; 2.00 A; A=148-242.
DR PDB; 2P22; X-ray; 2.70 A; B=1-118.
DR PDBsum; 2CAZ; -.
DR PDBsum; 2F66; -.
DR PDBsum; 2F6M; -.
DR PDBsum; 2G3K; -.
DR PDBsum; 2J9U; -.
DR PDBsum; 2J9V; -.
DR PDBsum; 2P22; -.
DR AlphaFoldDB; Q02767; -.
DR SMR; Q02767; -.
DR BioGRID; 36114; 110.
DR ComplexPortal; CPX-940; ESCRT-I complex.
DR DIP; DIP-5828N; -.
DR IntAct; Q02767; 6.
DR MINT; Q02767; -.
DR STRING; 4932.YPL065W; -.
DR TCDB; 3.A.31.1.1; the endosomal sorting complexes required for transport iii (escrt-iii) family.
DR iPTMnet; Q02767; -.
DR MaxQB; Q02767; -.
DR PaxDb; Q02767; -.
DR PRIDE; Q02767; -.
DR EnsemblFungi; YPL065W_mRNA; YPL065W; YPL065W.
DR GeneID; 856040; -.
DR KEGG; sce:YPL065W; -.
DR SGD; S000005986; VPS28.
DR VEuPathDB; FungiDB:YPL065W; -.
DR eggNOG; KOG3284; Eukaryota.
DR GeneTree; ENSGT00390000007486; -.
DR HOGENOM; CLU_076417_0_0_1; -.
DR InParanoid; Q02767; -.
DR OMA; CDEFPTV; -.
DR BioCyc; YEAST:G3O-33974-MON; -.
DR Reactome; R-SCE-917729; Endosomal Sorting Complex Required For Transport (ESCRT).
DR EvolutionaryTrace; Q02767; -.
DR PRO; PR:Q02767; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q02767; protein.
DR GO; GO:0005829; C:cytosol; HDA:SGD.
DR GO; GO:0005768; C:endosome; IDA:SGD.
DR GO; GO:0000813; C:ESCRT I complex; IDA:SGD.
DR GO; GO:0031902; C:late endosome membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0044877; F:protein-containing complex binding; IDA:SGD.
DR GO; GO:1904669; P:ATP export; IMP:SGD.
DR GO; GO:0006612; P:protein targeting to membrane; IMP:SGD.
DR GO; GO:0006623; P:protein targeting to vacuole; IMP:SGD.
DR GO; GO:0043328; P:protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway; IBA:GO_Central.
DR GO; GO:0043162; P:ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway; IDA:ComplexPortal.
DR Gene3D; 1.20.120.1130; -; 1.
DR Gene3D; 1.20.1440.200; -; 1.
DR InterPro; IPR037202; ESCRT_assembly_dom.
DR InterPro; IPR007143; Vps28.
DR InterPro; IPR017899; VPS28_C.
DR InterPro; IPR037206; VPS28_C_sf.
DR InterPro; IPR017898; VPS28_N.
DR InterPro; IPR038358; VPS28_N_sf.
DR PANTHER; PTHR12937; PTHR12937; 1.
DR Pfam; PF03997; VPS28; 1.
DR PIRSF; PIRSF017535; VPS28; 1.
DR SUPFAM; SSF140111; SSF140111; 1.
DR SUPFAM; SSF140427; SSF140427; 1.
DR PROSITE; PS51310; VPS28_C; 1.
DR PROSITE; PS51313; VPS28_N; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Endosome; Membrane; Protein transport;
KW Reference proteome; Transport.
FT CHAIN 1..242
FT /note="Vacuolar protein sorting-associated protein 28"
FT /id="PRO_0000120958"
FT DOMAIN 11..125
FT /note="VPS28 N-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00645"
FT DOMAIN 148..242
FT /note="VPS28 C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00642"
FT REGION 148..242
FT /note="Interaction with VSP36 and VPS20"
FT /evidence="ECO:0000269|PubMed:16749904"
FT MUTAGEN 40
FT /note="L->D: Abolishes ESCRT-I complex assembly; class E
FT phenotype (malformed late MVB); when associated with D-44."
FT /evidence="ECO:0000269|PubMed:16615894"
FT MUTAGEN 44
FT /note="Y->D: Abolishes ESCRT-I complex assembly; class E
FT phenotype (malformed late MVB); when associated with D-40."
FT /evidence="ECO:0000269|PubMed:16615894"
FT MUTAGEN 228..231
FT /note="FDLE->ASLA: Abolishes interaction with VPS20."
FT /evidence="ECO:0000269|PubMed:16749904"
FT CONFLICT 193
FT /note="R -> K (in Ref. 4; AAT92809)"
FT /evidence="ECO:0000305"
FT STRAND 10..12
FT /evidence="ECO:0007829|PDB:2P22"
FT HELIX 14..17
FT /evidence="ECO:0007829|PDB:2F6M"
FT STRAND 27..29
FT /evidence="ECO:0007829|PDB:2P22"
FT HELIX 31..58
FT /evidence="ECO:0007829|PDB:2F6M"
FT HELIX 64..82
FT /evidence="ECO:0007829|PDB:2F6M"
FT TURN 85..88
FT /evidence="ECO:0007829|PDB:2F6M"
FT HELIX 89..103
FT /evidence="ECO:0007829|PDB:2F6M"
FT HELIX 109..117
FT /evidence="ECO:0007829|PDB:2F6M"
FT HELIX 150..168
FT /evidence="ECO:0007829|PDB:2J9U"
FT HELIX 174..191
FT /evidence="ECO:0007829|PDB:2J9U"
FT HELIX 199..210
FT /evidence="ECO:0007829|PDB:2J9U"
FT HELIX 220..240
FT /evidence="ECO:0007829|PDB:2J9U"
SQ SEQUENCE 242 AA; 27702 MW; DE091D3F60C9D132 CRC64;
MQKHNIKLNQ NQDISQLFHD EVPLFDNSIT SKDKEVIETL SEIYSIVITL DHVEKAYLKD
SIDDTQYTNT VDKLLKQFKV YLNSQNKEEI NKHFQSIEAF CDTYNITASN AITRLERGIP
ITAEHAISTT TSAPSGDNKQ SSSSDKKFNA KYVAEATGNF ITVMDALKLN YNAKDQLHPL
LAELLISINR VTRDDFENRS KLIDWIVRIN KLSIGDTLTE TQIRELLFDL ELAYKSFYAL
LD
