ID   DSK2_YEAST              Reviewed;         373 AA.
AC   P48510; D6W0A3;
DT   01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT   05-OCT-2010, sequence version 2.
DT   27-MAR-2024, entry version 194.
DE   RecName: Full=Ubiquitin domain-containing protein DSK2;
GN   Name=DSK2; Synonyms=SHE4; OrderedLocusNames=YMR276W;
GN   ORFNames=YM8021.02;
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].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=8682868; DOI=10.1083/jcb.133.6.1331;
RA   Biggins S., Ivanovska I., Rose M.D.;
RT   "Yeast ubiquitin-like genes are involved in duplication of the microtubule
RT   organizing center.";
RL   J. Cell Biol. 133:1331-1346(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169872;
RA   Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA   Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA   Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA   Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL   Nature 387:90-93(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   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   [5]
RP   IDENTIFICATION BY MASS 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   [6]
RP   UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-13 AND LYS-76, AND
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=22106047; DOI=10.1002/pmic.201100166;
RA   Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
RT   "Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
RL   Proteomics 12:236-240(2012).
RN   [7]
RP   STRUCTURE BY NMR OF 328-373.
RX   PubMed=15837191; DOI=10.1016/j.str.2005.01.011;
RA   Ohno A., Jee J., Fujiwara K., Tenno T., Goda N., Tochio H., Kobayashi H.,
RA   Hiroaki H., Shirakawa M.;
RT   "Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular
RT   determinants for ubiquitin recognition.";
RL   Structure 13:521-532(2005).
CC   -!- FUNCTION: Involved, with RAD23 in spindle pole body duplication.
CC       Involved in the ubiquitin-proteasome proteolytic pathway.
CC   -!- INTERACTION:
CC       P48510; P34222: PTH2; NbExp=11; IntAct=EBI-6174, EBI-2345448;
CC       P48510; P38886: RPN10; NbExp=5; IntAct=EBI-6174, EBI-15949;
CC       P48510; O13563: RPN13; NbExp=8; IntAct=EBI-6174, EBI-32948;
CC       P48510; P33299: RPT1; NbExp=3; IntAct=EBI-6174, EBI-13910;
CC       P48510; P0CG63: UBI4; NbExp=3; IntAct=EBI-6174, EBI-7000452;
CC       P48510; Q16186: ADRM1; Xeno; NbExp=4; IntAct=EBI-6174, EBI-954387;
CC       P48510; O48726: RPN13; Xeno; NbExp=4; IntAct=EBI-6174, EBI-7710745;
CC       P48510; P0CG48: UBC; Xeno; NbExp=2; IntAct=EBI-6174, EBI-3390054;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC   -!- MISCELLANEOUS: Present with 3930 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; L40587; AAB07267.1; -; Genomic_DNA.
DR   EMBL; Z49704; CAA89774.1; -; Genomic_DNA.
DR   EMBL; BK006946; DAA10177.1; -; Genomic_DNA.
DR   PIR; S54583; S54583.
DR   RefSeq; NP_014003.1; NM_001182783.1.
DR   PDB; 1WR1; NMR; -; B=328-373.
DR   PDB; 2BWB; X-ray; 2.30 A; A/B/C/D/E/F/G/H/I=328-371.
DR   PDB; 2BWE; X-ray; 3.10 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R=328-373, S/T/U=1-75.
DR   PDB; 2BWF; X-ray; 1.15 A; A/B=1-75.
DR   PDB; 3M63; X-ray; 2.40 A; B=1-75.
DR   PDB; 4UN2; X-ray; 1.51 A; B=328-373.
DR   PDBsum; 1WR1; -.
DR   PDBsum; 2BWB; -.
DR   PDBsum; 2BWE; -.
DR   PDBsum; 2BWF; -.
DR   PDBsum; 3M63; -.
DR   PDBsum; 4UN2; -.
DR   AlphaFoldDB; P48510; -.
DR   BMRB; P48510; -.
DR   SMR; P48510; -.
DR   BioGRID; 35455; 144.
DR   DIP; DIP-4398N; -.
DR   IntAct; P48510; 25.
DR   MINT; P48510; -.
DR   STRING; 4932.YMR276W; -.
DR   iPTMnet; P48510; -.
DR   MaxQB; P48510; -.
DR   PaxDb; 4932-YMR276W; -.
DR   PeptideAtlas; P48510; -.
DR   EnsemblFungi; YMR276W_mRNA; YMR276W; YMR276W.
DR   GeneID; 855319; -.
DR   KEGG; sce:YMR276W; -.
DR   AGR; SGD:S000004889; -.
DR   SGD; S000004889; DSK2.
DR   VEuPathDB; FungiDB:YMR276W; -.
DR   eggNOG; KOG0010; Eukaryota.
DR   GeneTree; ENSGT00940000175001; -.
DR   HOGENOM; CLU_024293_0_1_1; -.
DR   InParanoid; P48510; -.
DR   OMA; PGMDMFG; -.
DR   OrthoDB; 3177594at2759; -.
DR   BioCyc; YEAST:G3O-32947-MONOMER; -.
DR   Reactome; R-SCE-8856825; Cargo recognition for clathrin-mediated endocytosis.
DR   BioGRID-ORCS; 855319; 6 hits in 10 CRISPR screens.
DR   EvolutionaryTrace; P48510; -.
DR   PRO; PR:P48510; -.
DR   Proteomes; UP000002311; Chromosome XIII.
DR   RNAct; P48510; Protein.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0005634; C:nucleus; IC:SGD.
DR   GO; GO:0031593; F:polyubiquitin modification-dependent protein binding; IBA:GO_Central.
DR   GO; GO:0030674; F:protein-macromolecule adaptor activity; IMP:SGD.
DR   GO; GO:0072665; P:protein localization to vacuole; IMP:SGD.
DR   GO; GO:0030474; P:spindle pole body duplication; IGI:SGD.
DR   GO; GO:0030433; P:ubiquitin-dependent ERAD pathway; IMP:SGD.
DR   GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IBA:GO_Central.
DR   CDD; cd14324; UBA_Dsk2p_like; 1.
DR   CDD; cd16106; Ubl_Dsk2p_like; 1.
DR   Gene3D; 1.10.8.10; DNA helicase RuvA subunit, C-terminal domain; 1.
DR   InterPro; IPR006636; STI1_HS-bd.
DR   InterPro; IPR015940; UBA.
DR   InterPro; IPR009060; UBA-like_sf.
DR   InterPro; IPR015496; Ubiquilin.
DR   InterPro; IPR000626; Ubiquitin-like_dom.
DR   InterPro; IPR029071; Ubiquitin-like_domsf.
DR   InterPro; IPR019954; Ubiquitin_CS.
DR   PANTHER; PTHR10677:SF3; FI07626P-RELATED; 1.
DR   PANTHER; PTHR10677; UBIQUILIN; 1.
DR   Pfam; PF00240; ubiquitin; 1.
DR   SMART; SM00727; STI1; 2.
DR   SMART; SM00165; UBA; 1.
DR   SMART; SM00213; UBQ; 1.
DR   SUPFAM; SSF46934; UBA-like; 1.
DR   SUPFAM; SSF54236; Ubiquitin-like; 1.
DR   PROSITE; PS50030; UBA; 1.
DR   PROSITE; PS00299; UBIQUITIN_1; 1.
DR   PROSITE; PS50053; UBIQUITIN_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Isopeptide bond; Nucleus; Reference proteome;
KW   Ubl conjugation.
FT   CHAIN           1..373
FT                   /note="Ubiquitin domain-containing protein DSK2"
FT                   /id="PRO_0000114900"
FT   DOMAIN          1..76
FT                   /note="Ubiquitin-like"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT   DOMAIN          327..371
FT                   /note="UBA"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT   REGION          221..270
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        245..270
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   CROSSLNK        13
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in ubiquitin)"
FT                   /evidence="ECO:0007744|PubMed:22106047"
FT   CROSSLNK        76
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in ubiquitin)"
FT                   /evidence="ECO:0007744|PubMed:22106047"
FT   CONFLICT        109
FT                   /note="A -> R (in Ref. 1; AAB07267)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        296
FT                   /note="A -> R (in Ref. 1; AAB07267)"
FT                   /evidence="ECO:0000305"
FT   STRAND          1..9
FT                   /evidence="ECO:0007829|PDB:2BWF"
FT   STRAND          12..18
FT                   /evidence="ECO:0007829|PDB:2BWF"
FT   HELIX           24..35
FT                   /evidence="ECO:0007829|PDB:2BWF"
FT   HELIX           39..41
FT                   /evidence="ECO:0007829|PDB:2BWF"
FT   STRAND          42..46
FT                   /evidence="ECO:0007829|PDB:2BWF"
FT   HELIX           58..60
FT                   /evidence="ECO:0007829|PDB:2BWF"
FT   STRAND          67..72
FT                   /evidence="ECO:0007829|PDB:2BWF"
FT   HELIX           328..331
FT                   /evidence="ECO:0007829|PDB:4UN2"
FT   HELIX           333..341
FT                   /evidence="ECO:0007829|PDB:4UN2"
FT   HELIX           347..357
FT                   /evidence="ECO:0007829|PDB:4UN2"
FT   HELIX           361..368
FT                   /evidence="ECO:0007829|PDB:4UN2"
SQ   SEQUENCE   373 AA;  39346 MW;  3F8691BB95E46569 CRC64;
     MSLNIHIKSG QDKWEVNVAP ESTVLQFKEA INKANGIPVA NQRLIYSGKI LKDDQTVESY
     HIQDGHSVHL VKSQPKPQTA SAAGANNATA TGAAAGTGAT PNMSSGQSAG FNPLADLTSA
     RYAGYLNMPS ADMFGPDGGA LNNDSNNQDE LLRMMENPIF QSQMNEMLSN PQMLDFMIQS
     NPQLQAMGPQ ARQMLQSPMF RQMLTNPDMI RQSMQFARMM DPNAGMGSAG GAASAFPAPG
     GDAPEEGSNT NTTSSSNTGN NAGTNAGTNA GANTAANPFA SLLNPALNPF ANAGNAASTG
     MPAFDPALLA SMFQPPVQAS QAEDTRPPEE RYEHQLRQLN DMGFFDFDRN VAALRRSGGS
     VQGALDSLLN GDV
//