GID4_YEAST
ID GID4_YEAST Reviewed; 362 AA.
AC P38263; D6VQA4;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 166.
DE RecName: Full=Vacuolar import and degradation protein 24;
DE AltName: Full=Glucose-induced degradation protein 4;
GN Name=VID24 {ECO:0000303|PubMed:9508768};
GN Synonyms=GID4 {ECO:0000303|PubMed:12686616}; OrderedLocusNames=YBR105C;
GN ORFNames=YBR0834;
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], FUNCTION, SUBCELLULAR LOCATION, AND
RP INDUCTION BY GLUCOSE.
RX PubMed=9508768; DOI=10.1083/jcb.140.6.1347;
RA Chiang M.C., Chiang H.L.;
RT "Vid24p, a novel protein localized to the fructose-1, 6-bisphosphatase-
RT containing vesicles, regulates targeting of fructose-1,6-bisphosphatase
RT from the vesicles to the vacuole for degradation.";
RL J. Cell Biol. 140:1347-1356(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7900426; DOI=10.1002/yea.320101014;
RA Mannhaupt G., Stucka R., Ehnle S., Vetter I., Feldmann H.;
RT "Analysis of a 70 kb region on the right arm of yeast chromosome II.";
RL Yeast 10:1363-1381(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA Mewes H.-W., Kleine K.;
RT "Complete DNA sequence of yeast chromosome II.";
RL EMBO J. 13:5795-5809(1994).
RN [4]
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 [5]
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 [6]
RP FUNCTION.
RX PubMed=12686616; DOI=10.1091/mbc.e02-08-0456;
RA Regelmann J., Schuele T., Josupeit F.S., Horak J., Rose M., Entian K.-D.,
RA Thumm M., Wolf D.H.;
RT "Catabolite degradation of fructose-1,6-bisphosphatase in the yeast
RT Saccharomyces cerevisiae: a genome-wide screen identifies eight novel GID
RT genes and indicates the existence of two degradation pathways.";
RL Mol. Biol. Cell 14:1652-1663(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 FUNCTION, INDUCTION BY GLUCOSE, AND UBIQUITINATION.
RX PubMed=18508925; DOI=10.1091/mbc.e08-03-0328;
RA Santt O., Pfirrmann T., Braun B., Juretschke J., Kimmig P., Scheel H.,
RA Hofmann K., Thumm M., Wolf D.H.;
RT "The yeast GID complex, a novel ubiquitin ligase (E3) involved in the
RT regulation of carbohydrate metabolism.";
RL Mol. Biol. Cell 19:3323-3333(2008).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-27, 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).
RN [10]
RP SUBUNIT.
RX PubMed=22645139; DOI=10.1074/jbc.m112.363762;
RA Menssen R., Schweiggert J., Schreiner J., Kusevic D., Reuther J., Braun B.,
RA Wolf D.H.;
RT "Exploring the topology of the Gid complex, the E3 ubiquitin ligase
RT involved in catabolite-induced degradation of gluconeogenic enzymes.";
RL J. Biol. Chem. 287:25602-25614(2012).
RN [11]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-20, AND IDENTIFICATION BY MASS
RP 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 [12]
RP FUNCTION.
RX PubMed=28126757; DOI=10.1126/science.aal3655;
RA Chen S.J., Wu X., Wadas B., Oh J.H., Varshavsky A.;
RT "An N-end rule pathway that recognizes proline and destroys gluconeogenic
RT enzymes.";
RL Science 355:0-0(2017).
CC -!- FUNCTION: Substrate-recognition component of the GID complex, a
CC multisubunit ubiquitin ligase that targets enzymes involved in
CC gluconeogenesis for proteasomal degradation when cells are shifted to
CC glucose-containing medium (PubMed:12686616, PubMed:18508925,
CC PubMed:28126757). Specific for substrates with an N-terminal Pro
CC (Pro/N-degron), including FBP1, ICL1 and MDH2 (PubMed:28126757). Has
CC high affinity for the N-terminal sequence Pro-Thr-Leu-Val, and can bind
CC peptides with an N-terminal sequence of the type Pro-
CC [Gly,Ala,Ser,Thr,Asp,Asn,Tyr,His]-[Ala,Val,Leu,Ile,Lys,Arg]-
CC [Val,Cys,Pro,Leu,Ile,Trp] (PubMed:28126757). Required for vacuolar
CC degradation of FBP1 when cells are shifted to glucose-containing
CC medium, probably by targeting FBP1-containing vesicles to the vacuole,
CC but is not required for FBP1 sequestration in cytoplasmic vesicles
CC (PubMed:9508768). {ECO:0000269|PubMed:12686616,
CC ECO:0000269|PubMed:18508925, ECO:0000269|PubMed:28126757,
CC ECO:0000269|PubMed:9508768}.
CC -!- SUBUNIT: Substrate-recognition component of the GID ubiquitin ligase
CC complex; interacts with proteins that have an N-terminal Pro/N-degron,
CC including FBP1, ICL1 and MDH2 (PubMed:28126757). Identified in the GID
CC complex, but only when cells are shifted to glucose-containing medium.
CC In the absence of glucose, the complex contains VID30/GID1, the E3
CC ubiquitin-ligase RMD5/GID2, VID28/GID5, GID7, GID8, and FYV10/GID9.
CC When cells are shifted to glucose-containing medium, VID24/GID4 is
CC recruited to the complex via interaction with VID28/GID5
CC (PubMed:22645139). {ECO:0000269|PubMed:22645139,
CC ECO:0000269|PubMed:28126757}.
CC -!- SUBCELLULAR LOCATION: Cytoplasmic vesicle membrane
CC {ECO:0000269|PubMed:9508768}; Peripheral membrane protein
CC {ECO:0000269|PubMed:9508768}. Note=Colocalizes with FBPase-containing
CC vesicles. {ECO:0000269|PubMed:9508768}.
CC -!- INDUCTION: Rapidly induced by a shift to glucose-containing medium.
CC {ECO:0000269|PubMed:18508925, ECO:0000269|PubMed:9508768}.
CC -!- PTM: Ubiquitinated by the GID complex, leading to subsequent
CC proteasomal degradation. {ECO:0000269|PubMed:18508925}.
CC -!- MISCELLANEOUS: Present with 6650 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the GID4/VID24 family. {ECO:0000305}.
CC -!- SIMILARITY: To yeast YGR066c and S.pombe SpAC3H1.14. {ECO:0000305}.
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DR EMBL; U86750; AAC23706.1; -; Genomic_DNA.
DR EMBL; X78993; CAA55608.1; -; Genomic_DNA.
DR EMBL; Z35974; CAA85060.1; -; Genomic_DNA.
DR EMBL; AY693057; AAT93076.1; -; Genomic_DNA.
DR EMBL; BK006936; DAA07224.1; -; Genomic_DNA.
DR PIR; S48270; S48270.
DR RefSeq; NP_009663.1; NM_001178453.1.
DR PDB; 6SWY; EM; 3.20 A; 4=1-362.
DR PDBsum; 6SWY; -.
DR AlphaFoldDB; P38263; -.
DR SMR; P38263; -.
DR BioGRID; 32809; 346.
DR ComplexPortal; CPX-301; GID ubiquitin ligase complex.
DR DIP; DIP-4502N; -.
DR IntAct; P38263; 24.
DR MINT; P38263; -.
DR STRING; 4932.YBR105C; -.
DR iPTMnet; P38263; -.
DR MaxQB; P38263; -.
DR PaxDb; P38263; -.
DR PRIDE; P38263; -.
DR EnsemblFungi; YBR105C_mRNA; YBR105C; YBR105C.
DR GeneID; 852402; -.
DR KEGG; sce:YBR105C; -.
DR SGD; S000000309; VID24.
DR VEuPathDB; FungiDB:YBR105C; -.
DR eggNOG; KOG4635; Eukaryota.
DR GeneTree; ENSGT00500000044930; -.
DR HOGENOM; CLU_028759_3_0_1; -.
DR InParanoid; P38263; -.
DR OMA; NILGFYY; -.
DR BioCyc; YEAST:G3O-29067-MON; -.
DR PRO; PR:P38263; -.
DR Proteomes; UP000002311; Chromosome II.
DR RNAct; P38263; protein.
DR GO; GO:0031410; C:cytoplasmic vesicle; IDA:SGD.
DR GO; GO:0030659; C:cytoplasmic vesicle membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; HDA:SGD.
DR GO; GO:0019898; C:extrinsic component of membrane; IDA:SGD.
DR GO; GO:0034657; C:GID complex; IDA:SGD.
DR GO; GO:0005773; C:vacuole; IEA:GOC.
DR GO; GO:0045721; P:negative regulation of gluconeogenesis; IMP:UniProtKB.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IMP:SGD.
DR GO; GO:0007039; P:protein catabolic process in the vacuole; IMP:SGD.
DR GO; GO:0006623; P:protein targeting to vacuole; IMP:SGD.
DR GO; GO:0071596; P:ubiquitin-dependent protein catabolic process via the N-end rule pathway; IMP:UniProtKB.
DR InterPro; IPR018618; Vacuolar_import/degrad_Vid24.
DR Pfam; PF09783; Vac_ImportDeg; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasmic vesicle; Isopeptide bond; Membrane;
KW Phosphoprotein; Protein transport; Reference proteome; Transport;
KW Ubl conjugation; Ubl conjugation pathway.
FT CHAIN 1..362
FT /note="Vacuolar import and degradation protein 24"
FT /id="PRO_0000065826"
FT REGION 1..40
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 240..267
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 133
FT /note="Interaction with the N-terminal Pro (Pro/N-degron)
FT of proteins that are targeted for degradation"
FT /evidence="ECO:0000250|UniProtKB:Q8IVV7"
FT SITE 294
FT /note="Interaction with the N-terminal Pro (Pro/N-degron)
FT of proteins that are targeted for degradation"
FT /evidence="ECO:0000250|UniProtKB:Q8IVV7"
FT SITE 316
FT /note="Interaction with the N-terminal Pro (Pro/N-degron)
FT of proteins that are targeted for degradation"
FT /evidence="ECO:0000250|UniProtKB:Q8IVV7"
FT MOD_RES 27
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT CROSSLNK 20
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
FT HELIX 93..96
FT /evidence="ECO:0007829|PDB:6SWY"
FT STRAND 128..135
FT /evidence="ECO:0007829|PDB:6SWY"
FT STRAND 138..149
FT /evidence="ECO:0007829|PDB:6SWY"
FT STRAND 162..169
FT /evidence="ECO:0007829|PDB:6SWY"
FT STRAND 179..187
FT /evidence="ECO:0007829|PDB:6SWY"
FT STRAND 190..193
FT /evidence="ECO:0007829|PDB:6SWY"
FT TURN 204..208
FT /evidence="ECO:0007829|PDB:6SWY"
FT HELIX 213..220
FT /evidence="ECO:0007829|PDB:6SWY"
FT HELIX 224..229
FT /evidence="ECO:0007829|PDB:6SWY"
FT HELIX 272..276
FT /evidence="ECO:0007829|PDB:6SWY"
FT STRAND 284..298
FT /evidence="ECO:0007829|PDB:6SWY"
FT STRAND 315..321
FT /evidence="ECO:0007829|PDB:6SWY"
FT TURN 322..324
FT /evidence="ECO:0007829|PDB:6SWY"
FT STRAND 326..332
FT /evidence="ECO:0007829|PDB:6SWY"
FT STRAND 339..344
FT /evidence="ECO:0007829|PDB:6SWY"
SQ SEQUENCE 362 AA; 41245 MW; FF020B239676E0B2 CRC64;
MINNPKVDSV AEKPKAVTSK QSEQAASPEP TPAPPVSRNQ YPITFNLTST APFHLHDRHR
YLQEQDLYKC ASRDSLSSLQ QLAHTPNGST RKKYIVEDQS PYSSENPVIV TSSYNHTVCT
NYLRPRMQFT GYQISGYKRY QVTVNLKTVD LPKKDCTSLS PHLSGFLSIR GLTNQHPEIS
TYFEAYAVNH KELGFLSSSW KDEPVLNEFK ATDQTDLEHW INFPSFRQLF LMSQKNGLNS
TDDNGTTNAA KKLPPQQLPT TPSADAGNIS RIFSQEKQFD NYLNERFIFM KWKEKFLVPD
ALLMEGVDGA SYDGFYYIVH DQVTGNIQGF YYHQDAEKFQ QLELVPSLKN KVESSDCSFE
FA
