RMD5_YEAST
ID RMD5_YEAST Reviewed; 421 AA.
AC Q12508; D6VSN5;
DT 01-FEB-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=E3 ubiquitin-protein ligase RMD5 {ECO:0000305};
DE EC=2.3.2.27 {ECO:0000269|PubMed:18508925, ECO:0000305|PubMed:12686616};
DE AltName: Full=Glucose-induced degradation protein 2;
DE AltName: Full=Required for meiotic nuclear division protein 5;
DE AltName: Full=Sporulation protein RMD5;
GN Name=RMD5; Synonyms=GID2; OrderedLocusNames=YDR255C; ORFNames=YD9320A.05c;
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=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(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.
RX PubMed=9737955; DOI=10.1074/jbc.273.39.25000;
RA Haemmerle M., Bauer J., Rose M., Szallies A., Thumm M., Duesterhus S.,
RA Mecke D., Entian K.D., Wolf D.H.;
RT "Proteins of newly isolated mutants and the amino-terminal proline are
RT essential for ubiquitin-proteasome-catalyzed catabolite degradation of
RT fructose-1,6-bisphosphatase of Saccharomyces cerevisiae.";
RL J. Biol. Chem. 273:25000-25005(1998).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY, AND PATHWAY.
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 [6]
RP FUNCTION, CATALYTIC ACTIVITY, PATHWAY, AND MUTAGENESIS OF CYS-379.
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 [7]
RP INTERACTION WITH FYV10.
RX PubMed=22044534; DOI=10.1016/j.febslet.2011.10.038;
RA Braun B., Pfirrmann T., Menssen R., Hofmann K., Scheel H., Wolf D.H.;
RT "Gid9, a second RING finger protein contributes to the ubiquitin ligase
RT activity of the Gid complex required for catabolite degradation.";
RL FEBS Lett. 585:3856-3861(2011).
RN [8]
RP SUBUNIT, AND INTERACTION WITH GID8 AND VID28.
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 [9]
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: E3 ubiquitin-protein ligase component of the GID complex
CC (PubMed:12686616, PubMed:18508925). Required for the adaptation to the
CC presence of glucose in the growth medium; mediates the degradation of
CC enzymes involved in gluconeogenesis when cells are shifted to glucose-
CC containing medium (PubMed:9737955, PubMed:18508925). Required for
CC proteasome-dependent catabolite degradation of fructose-1,6-
CC bisphosphatase (FBP1) (PubMed:9737955, PubMed:12686616,
CC PubMed:18508925, PubMed:28126757). {ECO:0000269|PubMed:12686616,
CC ECO:0000269|PubMed:18508925, ECO:0000269|PubMed:28126757,
CC ECO:0000269|PubMed:9737955}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC EC=2.3.2.27; Evidence={ECO:0000269|PubMed:18508925,
CC ECO:0000305|PubMed:12686616};
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC {ECO:0000269|PubMed:12686616, ECO:0000269|PubMed:18508925}.
CC -!- SUBUNIT: Identified in the GID complex. In the absence of glucose, the
CC complex contains VID30/GID1, the E3 ubiquitin-ligase RMD5/GID2,
CC VID28/GID5, GID7, GID8, and FYV10/GID9. When cells are shifted to
CC glucose-containing medium, VID24/GID4 is induced and becomes part of
CC the complex (PubMed:22645139). Interacts with FYV10/GID9; the
CC interaction is direct (PubMed:22044534). Within the GID complex,
CC interacts directly with GID8, FYV10/GID9 and VID28/GID5
CC (PubMed:22645139). {ECO:0000269|PubMed:22044534,
CC ECO:0000269|PubMed:22645139}.
CC -!- INTERACTION:
CC Q12508; P53076: VID30; NbExp=8; IntAct=EBI-38868, EBI-24173;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12686616}.
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DR EMBL; Z70202; CAA94094.1; -; Genomic_DNA.
DR EMBL; Z68329; CAA92712.1; -; Genomic_DNA.
DR EMBL; AY557796; AAS56122.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12095.1; -; Genomic_DNA.
DR PIR; S67312; S67312.
DR RefSeq; NP_010541.3; NM_001180563.3.
DR PDB; 7NS4; EM; 3.90 A; b=1-421.
DR PDBsum; 7NS4; -.
DR AlphaFoldDB; Q12508; -.
DR SMR; Q12508; -.
DR BioGRID; 32305; 80.
DR ComplexPortal; CPX-301; GID ubiquitin ligase complex.
DR DIP; DIP-1835N; -.
DR IntAct; Q12508; 6.
DR MINT; Q12508; -.
DR STRING; 4932.YDR255C; -.
DR MaxQB; Q12508; -.
DR PaxDb; Q12508; -.
DR PRIDE; Q12508; -.
DR TopDownProteomics; Q12508; -.
DR EnsemblFungi; YDR255C_mRNA; YDR255C; YDR255C.
DR GeneID; 851842; -.
DR KEGG; sce:YDR255C; -.
DR SGD; S000002663; RMD5.
DR VEuPathDB; FungiDB:YDR255C; -.
DR eggNOG; KOG2817; Eukaryota.
DR GeneTree; ENSGT00940000153203; -.
DR HOGENOM; CLU_020227_2_0_1; -.
DR InParanoid; Q12508; -.
DR OMA; PYSLPCH; -.
DR BioCyc; YEAST:G3O-29827-MON; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q12508; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q12508; protein.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0034657; C:GID complex; IDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0005777; C:peroxisome; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IDA:SGD.
DR GO; GO:0045721; P:negative regulation of gluconeogenesis; IMP:SGD.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IMP:SGD.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IMP:SGD.
DR CDD; cd16652; dRing_Rmd5p_like; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR024964; CTLH/CRA.
DR InterPro; IPR006595; CTLH_C.
DR InterPro; IPR045098; Fyv10_fam.
DR InterPro; IPR027711; Rmd5.
DR InterPro; IPR037683; Rmd5_dRing.
DR InterPro; IPR044063; ZF_RING_GID.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR12170; PTHR12170; 1.
DR PANTHER; PTHR12170:SF3; PTHR12170:SF3; 1.
DR Pfam; PF10607; CLTH; 1.
DR SMART; SM00668; CTLH; 1.
DR PROSITE; PS50897; CTLH; 1.
DR PROSITE; PS51867; ZF_RING_GID; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Metal-binding; Reference proteome; Transferase;
KW Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..421
FT /note="E3 ubiquitin-protein ligase RMD5"
FT /id="PRO_0000097361"
FT DOMAIN 176..236
FT /note="CTLH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00058"
FT ZN_FING 361..404
FT /note="RING-Gid-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01215"
FT MUTAGEN 379
FT /note="C->S: Abolishes FBP1 ubiquitination and
FT degradation."
FT /evidence="ECO:0000269|PubMed:18508925"
SQ SEQUENCE 421 AA; 49169 MW; B814479D30E072E3 CRC64;
MSELLDSFET EFAKFYTDSN LEETNLQKCL DHTHEFKSQL KKLKAHLNKH IQESKPEVYN
KLSDKEKQKF KRKRELIIEK LSKSQRQWDH SVKKQIKYVS QQSNRFNKST LNKLKEFDID
SVYVNKLPKE TMENVNEAIG YHILRYSIDN MPLGNKNEAF QYLKDVYGIT NKESTEFIEM
GQIVHDLKKG DTESCLKWCS NEMESLSSNH TALSSLKFDL YTLSAMQIVK HGNPVELYYQ
ITQNAPLDCF RHREKELMQN VVPLLTKSLI GQPIEDIDSK VNKELKECTS LFIKEYCAAK
HIFFDSPLFL IVLSGLISFQ FFIKYKTIRE LAHVDWTTKD ELPFDVKLPD FLTHFHPIFI
CPVLKEETTT ENPPYSLACH HIISKKALDR LSKNGTITFK CPYCPVNTSM SSTKKVRFVM
L
