EI2BD_YEAST
ID EI2BD_YEAST Reviewed; 651 AA.
AC P12754; D6VUL5;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1989, sequence version 1.
DT 03-AUG-2022, entry version 188.
DE RecName: Full=Translation initiation factor eIF-2B subunit delta;
DE AltName: Full=GCD complex subunit GCD2;
DE AltName: Full=Guanine nucleotide exchange factor subunit GCD2;
DE AltName: Full=eIF-2B GDP-GTP exchange factor subunit delta;
GN Name=GCD2; Synonyms=TIF224; OrderedLocusNames=YGR083C;
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=S288c / GRF88;
RX PubMed=2668117; DOI=10.1093/genetics/122.3.551;
RA Paddon C.J., Hanning E.M., Hinnebusch A.G.;
RT "Amino acid sequence similarity between GCN3 and GCD2, positive and
RT negative translational regulators of GCN4: evidence for antagonism by
RT competition.";
RL Genetics 122:551-559(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(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 IDENTIFICATION IN THE EIF2-B COMPLEX, AND FUNCTION OF THE EIF2-B COMPLEX.
RX PubMed=8506384; DOI=10.1073/pnas.90.11.5350;
RA Cigan A.M., Bushman J.L., Boal T.R., Hinnebusch A.G.;
RT "A protein complex of translational regulators of GCN4 mRNA is the guanine
RT nucleotide-exchange factor for translation initiation factor 2 in yeast.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:5350-5354(1993).
RN [5]
RP FUNCTION, AND IDENTIFICATION IN A EIF2-B SUBCOMPLEX.
RX PubMed=9472020; DOI=10.1101/gad.12.4.514;
RA Pavitt G.D., Ramaiah K.V., Kimball S.R., Hinnebusch A.G.;
RT "eIF2 independently binds two distinct eIF2B subcomplexes that catalyze and
RT regulate guanine-nucleotide exchange.";
RL Genes Dev. 12:514-526(1998).
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 ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE 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).
CC -!- FUNCTION: Acts as essential component of the translation initiation
CC factor 2B (eIF2-B or GCD complex), which catalyzes the exchange of
CC eukaryotic initiation factor 2 (eIF-2)-bound GDP for GTP and is
CC regulated by phosphorylated eIF-2. It activates the synthesis of GCN4
CC in yeast under amino acid starvation conditions by suppressing the
CC inhibitory effects of multiple AUG codons present in the leader of GCN4
CC mRNA. It may promote either repression or activation of GCN4 expression
CC depending on amino acid availability. GCD2 is also required for cell
CC viability. Its function can partially be replaced by GCN3 under normal
CC growth conditions in GCD2-defective mutants, under AA starvation
CC conditions GCN3 is an antagonist (GCN4 translational activator).
CC {ECO:0000269|PubMed:8506384, ECO:0000269|PubMed:9472020}.
CC -!- SUBUNIT: Translation initiation factor 2B (eIF2-B) is composed of five
CC different subunits; alpha (GCN3), beta (GCD7), gamma (GCD1), delta
CC (GCD2) and epsilon (GCD6). A regulatory subcomplex comprising GCN3,
CC GCD7 and GCD2 interacts preferentially with phosphorylated eIF-2 and
CC has no exchange activity in vitro. {ECO:0000269|PubMed:8506384,
CC ECO:0000269|PubMed:9472020}.
CC -!- INTERACTION:
CC P12754; P32502: GCD7; NbExp=10; IntAct=EBI-6265, EBI-6260;
CC P12754; P14741: GCN3; NbExp=7; IntAct=EBI-6265, EBI-6253;
CC -!- MISCELLANEOUS: Present with 10300 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the eIF-2B alpha/beta/delta subunits family.
CC {ECO:0000305}.
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DR EMBL; X15658; CAA33693.1; -; Genomic_DNA.
DR EMBL; Z72868; CAA97085.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08176.1; -; Genomic_DNA.
DR PIR; S05809; RGBYD2.
DR RefSeq; NP_011597.1; NM_001181212.1.
DR PDB; 6I3M; EM; 3.93 A; C/D=1-651.
DR PDB; 6I7T; EM; 4.61 A; C/D=1-651.
DR PDB; 6QG0; EM; 4.20 A; G/H=1-651.
DR PDB; 6QG1; EM; 4.20 A; G/H=1-651.
DR PDB; 6QG2; EM; 4.60 A; G/H=1-651.
DR PDB; 6QG3; EM; 9.40 A; G/H=1-651.
DR PDB; 6QG5; EM; 10.10 A; G/H=1-651.
DR PDB; 6QG6; EM; 4.65 A; G/H=1-651.
DR PDBsum; 6I3M; -.
DR PDBsum; 6I7T; -.
DR PDBsum; 6QG0; -.
DR PDBsum; 6QG1; -.
DR PDBsum; 6QG2; -.
DR PDBsum; 6QG3; -.
DR PDBsum; 6QG5; -.
DR PDBsum; 6QG6; -.
DR AlphaFoldDB; P12754; -.
DR SMR; P12754; -.
DR BioGRID; 33325; 132.
DR ComplexPortal; CPX-429; Eukaryotic translation initiation factor 2B complex.
DR DIP; DIP-2343N; -.
DR IntAct; P12754; 30.
DR MINT; P12754; -.
DR STRING; 4932.YGR083C; -.
DR iPTMnet; P12754; -.
DR MaxQB; P12754; -.
DR PaxDb; P12754; -.
DR PRIDE; P12754; -.
DR EnsemblFungi; YGR083C_mRNA; YGR083C; YGR083C.
DR GeneID; 852974; -.
DR KEGG; sce:YGR083C; -.
DR SGD; S000003315; GCD2.
DR VEuPathDB; FungiDB:YGR083C; -.
DR eggNOG; KOG1467; Eukaryota.
DR GeneTree; ENSGT00550000075009; -.
DR HOGENOM; CLU_016218_3_4_1; -.
DR InParanoid; P12754; -.
DR OMA; IPRCIAM; -.
DR BioCyc; YEAST:G3O-30795-MON; -.
DR Reactome; R-SCE-72731; Recycling of eIF2:GDP.
DR PRO; PR:P12754; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P12754; protein.
DR GO; GO:0005829; C:cytosol; HDA:SGD.
DR GO; GO:0005851; C:eukaryotic translation initiation factor 2B complex; IDA:SGD.
DR GO; GO:0032045; C:guanyl-nucleotide exchange factor complex; IDA:SGD.
DR GO; GO:0030234; F:enzyme regulator activity; IDA:SGD.
DR GO; GO:0003743; F:translation initiation factor activity; IMP:SGD.
DR GO; GO:0043547; P:positive regulation of GTPase activity; IDA:ComplexPortal.
DR GO; GO:0006446; P:regulation of translational initiation; IDA:SGD.
DR Gene3D; 3.40.50.10470; -; 1.
DR InterPro; IPR000649; IF-2B-related.
DR InterPro; IPR042529; IF_2B-like_C.
DR InterPro; IPR037171; NagB/RpiA_transferase-like.
DR Pfam; PF01008; IF-2B; 1.
DR SUPFAM; SSF100950; SSF100950; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Initiation factor; Phosphoprotein;
KW Protein biosynthesis; Reference proteome; Repressor;
KW Translation regulation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CHAIN 2..651
FT /note="Translation initiation factor eIF-2B subunit delta"
FT /id="PRO_0000156072"
FT REGION 1..108
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 566..600
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..31
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 33..51
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 69..108
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 566..595
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES 106
FT /note="Phosphoserine"
FT /evidence="ECO:0000255"
FT MOD_RES 121
FT /note="Phosphothreonine"
FT /evidence="ECO:0000255"
SQ SEQUENCE 651 AA; 70852 MW; B188457543CE1AAE CRC64;
MSESEAKSRS ATPPSKAKQA TPTTTAAANG EKKLTNKELK ELKKQEKAAK RAAMKQANGI
SIEQQQQQAQ MKKEKKQLQR EQQQKREQKQ KNANKKKQNE RNVKKSTLFG HLETTEERRA
TILALTSAVS SPKTSRITAA GLMVPVVASA LSGSNVLTAS SLMPVGPNAS STVSASAPAS
TTTTLPASSA ALSAGTSSAS TNTPTAIQQE IASSNASDVA KTLASISLEA GEFNVIPGIS
SVIPTVLEQS FDNSSLISSV KELLLNKDLI HPSILLLTSH LAHYKIVGSI PRCIAMLEVF
QIVIKDYQTP KGTTLSRNLT SYLSHQIDLL KKARPLSVTM GNAIRWLKQE ISLIDPSTPD
KAAKKDLCEK IGQFAKEKIE LADQLIIDNA STQIEESTTI VTYGSSKVLT ELLLHNAISL
KKNIKVIVVD SRPLFEGRKM AETLRNAGVN VMYALITSLD TIFNMDVDYV FLGAHSILSN
GFLYSRAGTA MLAMSAKRRN IPVLVCCESL KFSQRVQLDS VTFNELADPN DLVNIDYENP
VERRGNKGAL LNQFIKERKF EKKKLAMENK PKGNKIGGKK GSEGESKDAS NEEDSNSKNI
LDGWQELPSL NIVNILYDLT PPEYIKKVIT EFGALPPSSV PVILREYKGS A
