RPN13_YEAST
ID RPN13_YEAST Reviewed; 156 AA.
AC O13563; D6VZ57;
DT 12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 173.
DE RecName: Full=26S proteasome regulatory subunit RPN13;
DE AltName: Full=Proteasome non-ATPase subunit 13;
GN Name=RPN13; Synonyms=DAQ1; OrderedLocusNames=YLR421C;
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=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(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].
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 [4]
RP FUNCTION OF THE 26S PROTEASOME.
RX PubMed=7957966; DOI=10.1016/0014-5793(94)01177-x;
RA Fischer M., Hilt W., Richter-Ruoff B., Gonen H., Ciechanover A., Wolf D.H.;
RT "The 26S proteasome of the yeast Saccharomyces cerevisiae.";
RL FEBS Lett. 355:69-75(1994).
RN [5]
RP IDENTIFICATION IN THE 19S AND 26S PROTEASOMES, FUNCTION OF THE 26S
RP PROTEASOME, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=11029046; DOI=10.1091/mbc.11.10.3425;
RA Verma R., Chen S., Feldman R., Schieltz D., Yates J., Dohmen J.,
RA Deshaies R.J.;
RT "Proteasomal proteomics: identification of nucleotide-sensitive proteasome-
RT interacting proteins by mass spectrometric analysis of affinity-purified
RT proteasomes.";
RL Mol. Biol. Cell 11:3425-3439(2000).
RN [6]
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 [7]
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 [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-135 AND SER-140, 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 [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-135 AND SER-140, 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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-133; SER-135 AND SER-140, AND
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 [11]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, ACETYLATION [LARGE SCALE
RP ANALYSIS] AT SER-2 (ISOFORM 2), CLEAVAGE OF INITIATOR METHIONINE [LARGE
RP SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS]
RP (ISOFORM 2), AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
RP 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).
RN [12]
RP STRUCTURE BY ELECTRON MICROSCOPY (7.4 ANGSTROMS) OF THE 26S PROTEASOME.
RX PubMed=22927375; DOI=10.1073/pnas.1213333109;
RA Beck F., Unverdorben P., Bohn S., Schweitzer A., Pfeifer G., Sakata E.,
RA Nickell S., Plitzko J.M., Villa E., Baumeister W., Forster F.;
RT "Near-atomic resolution structural model of the yeast 26S proteasome.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:14870-14875(2012).
CC -!- FUNCTION: Component of the 19S cap proteasome complex which acts as a
CC regulatory subunit of the 26S proteasome, involved in the ATP-dependent
CC degradation of ubiquitinated proteins. {ECO:0000269|PubMed:11029046,
CC ECO:0000269|PubMed:7957966}.
CC -!- SUBUNIT: Component of the 19S cap proteasome complex composed of at
CC least RPN1, RPN2, RPN3, RPN4, RPN5, RPN6, RPN7, RPN8, RPN9, RPN10,
CC RPN11, RPN12, RPN13, RPT1, RPT2, RPT3, RPT4, RPT5, and RPT6. The 19S
CC subcomplex associates with the 20S proteasome subcomplex to form the
CC functional 26S proteasome. {ECO:0000269|PubMed:11029046}.
CC -!- INTERACTION:
CC O13563; P48510: DSK2; NbExp=8; IntAct=EBI-32948, EBI-6174;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative initiation; Named isoforms=2;
CC Name=1;
CC IsoId=O13563-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O13563-2; Sequence=VSP_058121;
CC -!- MISCELLANEOUS: Present with 12200 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RPN13 family. {ECO:0000305}.
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DR EMBL; U20939; AAB67511.1; -; Genomic_DNA.
DR EMBL; AY558321; AAS56647.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09723.1; -; Genomic_DNA.
DR PIR; S69319; S69319.
DR RefSeq; NP_013525.3; NM_001182309.3. [O13563-1]
DR PDB; 2Z4D; NMR; -; A=6-101.
DR PDB; 3JCO; EM; 4.80 A; X=1-156.
DR PDB; 3JCP; EM; 4.60 A; X=1-156.
DR PDB; 4CR2; EM; 7.70 A; X=1-156.
DR PDB; 4CR3; EM; 9.30 A; X=1-156.
DR PDB; 4CR4; EM; 8.80 A; X=1-156.
DR PDB; 5A5B; EM; 9.50 A; X=1-156.
DR PDB; 5MPB; EM; 7.80 A; X=1-156.
DR PDB; 5MPC; EM; 7.70 A; X=1-156.
DR PDB; 5MPD; EM; 4.10 A; X=1-156.
DR PDB; 5MPE; EM; 4.50 A; X=1-156.
DR PDB; 5WVI; EM; 6.30 A; X=1-156.
DR PDB; 5WVK; EM; 4.20 A; X=1-156.
DR PDB; 6FVT; EM; 4.10 A; X=7-133.
DR PDB; 6FVU; EM; 4.50 A; X=7-133.
DR PDB; 6FVV; EM; 5.40 A; X=7-133.
DR PDB; 6FVW; EM; 4.50 A; X=7-133.
DR PDB; 6FVX; EM; 4.90 A; X=7-133.
DR PDB; 6FVY; EM; 6.10 A; X=7-133.
DR PDB; 6J2C; EM; 7.00 A; X=1-156.
DR PDB; 6J2N; EM; 7.50 A; X=1-156.
DR PDB; 6J2Q; EM; 3.80 A; X=1-156.
DR PDB; 6J2X; EM; 3.80 A; X=1-156.
DR PDB; 6J30; EM; 4.50 A; X=1-156.
DR PDB; 7QO3; EM; 6.10 A; X=1-156.
DR PDB; 7QO5; EM; 6.00 A; X=1-156.
DR PDBsum; 2Z4D; -.
DR PDBsum; 3JCO; -.
DR PDBsum; 3JCP; -.
DR PDBsum; 4CR2; -.
DR PDBsum; 4CR3; -.
DR PDBsum; 4CR4; -.
DR PDBsum; 5A5B; -.
DR PDBsum; 5MPB; -.
DR PDBsum; 5MPC; -.
DR PDBsum; 5MPD; -.
DR PDBsum; 5MPE; -.
DR PDBsum; 5WVI; -.
DR PDBsum; 5WVK; -.
DR PDBsum; 6FVT; -.
DR PDBsum; 6FVU; -.
DR PDBsum; 6FVV; -.
DR PDBsum; 6FVW; -.
DR PDBsum; 6FVX; -.
DR PDBsum; 6FVY; -.
DR PDBsum; 6J2C; -.
DR PDBsum; 6J2N; -.
DR PDBsum; 6J2Q; -.
DR PDBsum; 6J2X; -.
DR PDBsum; 6J30; -.
DR PDBsum; 7QO3; -.
DR PDBsum; 7QO5; -.
DR AlphaFoldDB; O13563; -.
DR SMR; O13563; -.
DR BioGRID; 31680; 110.
DR ComplexPortal; CPX-2262; 26S Proteasome complex.
DR DIP; DIP-4637N; -.
DR IntAct; O13563; 34.
DR MINT; O13563; -.
DR STRING; 4932.YLR421C; -.
DR iPTMnet; O13563; -.
DR MaxQB; O13563; -.
DR PaxDb; O13563; -.
DR PRIDE; O13563; -.
DR EnsemblFungi; YLR421C_mRNA; YLR421C; YLR421C. [O13563-1]
DR GeneID; 851140; -.
DR KEGG; sce:YLR421C; -.
DR SGD; S000004413; RPN13.
DR VEuPathDB; FungiDB:YLR421C; -.
DR eggNOG; KOG3037; Eukaryota.
DR GeneTree; ENSGT00390000013839; -.
DR HOGENOM; CLU_115505_0_0_1; -.
DR InParanoid; O13563; -.
DR OMA; IPGETMW; -.
DR BioCyc; YEAST:G3O-32481-MON; -.
DR EvolutionaryTrace; O13563; -.
DR PRO; PR:O13563; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; O13563; protein.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0000502; C:proteasome complex; IPI:ComplexPortal.
DR GO; GO:0008541; C:proteasome regulatory particle, lid subcomplex; IDA:SGD.
DR GO; GO:0034515; C:proteasome storage granule; IDA:SGD.
DR GO; GO:0061133; F:endopeptidase activator activity; IBA:GO_Central.
DR GO; GO:0070628; F:proteasome binding; IBA:GO_Central.
DR GO; GO:0043130; F:ubiquitin binding; IDA:SGD.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IDA:ComplexPortal.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IMP:SGD.
DR Gene3D; 2.30.29.70; -; 1.
DR InterPro; IPR006773; Rpn13/ADRM1.
DR InterPro; IPR044868; Rpn13/ADRM1_Pru.
DR InterPro; IPR038633; Rpn13/ADRM1_Pru_sf.
DR PANTHER; PTHR12225; PTHR12225; 1.
DR Pfam; PF04683; Proteasom_Rpn13; 1.
DR PROSITE; PS51917; PRU; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative initiation; Cytoplasm; Nucleus;
KW Phosphoprotein; Proteasome; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CHAIN 2..156
FT /note="26S proteasome regulatory subunit RPN13"
FT /id="PRO_0000268704"
FT DOMAIN 2..132
FT /note="Pru"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01265"
FT REGION 128..156
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES 133
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 135
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MOD_RES 140
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT VAR_SEQ 1..2
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_058121"
FT STRAND 8..10
FT /evidence="ECO:0007829|PDB:2Z4D"
FT STRAND 15..18
FT /evidence="ECO:0007829|PDB:2Z4D"
FT TURN 19..22
FT /evidence="ECO:0007829|PDB:2Z4D"
FT STRAND 23..26
FT /evidence="ECO:0007829|PDB:2Z4D"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:2Z4D"
FT TURN 38..40
FT /evidence="ECO:0007829|PDB:2Z4D"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:2Z4D"
FT STRAND 46..52
FT /evidence="ECO:0007829|PDB:2Z4D"
FT STRAND 64..66
FT /evidence="ECO:0007829|PDB:2Z4D"
FT TURN 70..72
FT /evidence="ECO:0007829|PDB:2Z4D"
FT STRAND 73..77
FT /evidence="ECO:0007829|PDB:2Z4D"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:2Z4D"
FT STRAND 86..90
FT /evidence="ECO:0007829|PDB:2Z4D"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:2Z4D"
FT STRAND 97..100
FT /evidence="ECO:0007829|PDB:2Z4D"
FT INIT_MET O13563-2:1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES O13563-2:2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22814378"
SQ SEQUENCE 156 AA; 17902 MW; 752E8A12DC3799D4 CRC64;
MSMSSTVIKF RAGVCEYNED SRLCTPIPVQ GEIEIKPNEE EELGFWDFEW RPTEKPVGRE
LDPISLILIP GETMWVPIKS SKSGRIFALV FSSNERYFFW LQEKNSGNLP LNELSAKDKE
IYNKMIGVLN NSSESDEEES NDEKQKAQDV DVSMQD
