SYG2_YEAST
ID SYG2_YEAST Reviewed; 618 AA.
AC Q06817; D6W483;
DT 22-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 163.
DE RecName: Full=Glycine--tRNA ligase 2;
DE EC=6.1.1.14 {ECO:0000269|PubMed:23816885};
DE AltName: Full=Diadenosine tetraphosphate synthetase;
DE Short=Ap4A synthetase;
DE EC=2.7.7.- {ECO:0000250|UniProtKB:P41250};
DE AltName: Full=Glycyl-tRNA synthetase 2;
DE Short=GlyRS 2;
DE Short=GlyRS2;
GN Name=GRS2; OrderedLocusNames=YPR081C;
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=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(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 FUNCTION.
RX PubMed=10874035; DOI=10.1074/jbc.m003416200;
RA Turner R.J., Lovato M., Schimmel P.;
RT "One of two genes encoding glycyl-tRNA synthetase in Saccharomyces
RT cerevisiae provides mitochondrial and cytoplasmic functions.";
RL J. Biol. Chem. 275:27681-27688(2000).
RN [4]
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 [5]
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 [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [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).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=23816885; DOI=10.1128/mcb.00122-13;
RA Wu Y.H., Chang C.P., Chien C.I., Tseng Y.K., Wang C.C.;
RT "An insertion peptide in yeast glycyl-tRNA synthetase facilitates both
RT productive docking and catalysis of cognate tRNAs.";
RL Mol. Cell. Biol. 33:3515-3523(2013).
CC -!- FUNCTION: Catalyzes the ATP-dependent ligation of glycine to the 3'-end
CC of its cognate tRNA, via the formation of an aminoacyl-adenylate
CC intermediate (Gly-AMP) (PubMed:23816885). Also produces diadenosine
CC tetraphosphate (Ap4A), a universal pleiotropic signaling molecule
CC needed for cell regulation pathways, by direct condensation of 2 ATPs.
CC Thereby, may play a special role in Ap4A homeostasis (By similarity).
CC {ECO:0000250|UniProtKB:P41250, ECO:0000269|PubMed:23816885}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-
CC tRNA(Gly); Xref=Rhea:RHEA:16013, Rhea:RHEA-COMP:9664, Rhea:RHEA-
CC COMP:9683, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:57305,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:78522, ChEBI:CHEBI:456215;
CC EC=6.1.1.14; Evidence={ECO:0000269|PubMed:23816885};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:16014;
CC Evidence={ECO:0000305|PubMed:23816885};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 ATP + H(+) = diphosphate + P(1),P(4)-bis(5'-adenosyl)
CC tetraphosphate; Xref=Rhea:RHEA:34935, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:58141;
CC Evidence={ECO:0000250|UniProtKB:P41250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=145 uM for glycine (at 25 degrees Celsius)
CC {ECO:0000269|PubMed:23816885};
CC KM=0.53 uM for tRNA(Gly) (at 25 degrees Celsius)
CC {ECO:0000269|PubMed:23816885};
CC Note=kcat is 0.10 sec(-1) for the aminoacylation reaction (at 25
CC degrees Celsius). {ECO:0000269|PubMed:23816885};
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:P41250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 2290 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000305}.
CC -!- CAUTION: GRS1, which appears to be a duplication of GRS2, is necessary
CC and sufficient for both mitochondrial and cytoplasmic glycyl-tRNA
CC synthetase activities, suggesting that GRS2 may not be essential.
CC {ECO:0000305}.
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DR EMBL; U51033; AAB68130.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11499.1; -; Genomic_DNA.
DR PIR; S69067; S69067.
DR RefSeq; NP_015406.1; NM_001184178.1.
DR AlphaFoldDB; Q06817; -.
DR SMR; Q06817; -.
DR BioGRID; 36252; 58.
DR IntAct; Q06817; 6.
DR MINT; Q06817; -.
DR STRING; 4932.YPR081C; -.
DR MaxQB; Q06817; -.
DR PaxDb; Q06817; -.
DR PRIDE; Q06817; -.
DR EnsemblFungi; YPR081C_mRNA; YPR081C; YPR081C.
DR GeneID; 856196; -.
DR KEGG; sce:YPR081C; -.
DR SGD; S000006285; GRS2.
DR VEuPathDB; FungiDB:YPR081C; -.
DR eggNOG; KOG2298; Eukaryota.
DR GeneTree; ENSGT00940000153759; -.
DR HOGENOM; CLU_015515_1_0_1; -.
DR InParanoid; Q06817; -.
DR OMA; NDGFPAI; -.
DR BioCyc; YEAST:G3O-34225-MON; -.
DR BRENDA; 6.1.1.14; 984.
DR PRO; PR:Q06817; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q06817; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004820; F:glycine-tRNA ligase activity; IDA:SGD.
DR GO; GO:0046983; F:protein dimerization activity; ISS:UniProtKB.
DR GO; GO:0016740; F:transferase activity; IEA:UniProtKB-KW.
DR GO; GO:0015966; P:diadenosine tetraphosphate biosynthetic process; ISS:UniProtKB.
DR GO; GO:0006426; P:glycyl-tRNA aminoacylation; IGI:SGD.
DR GO; GO:0070150; P:mitochondrial glycyl-tRNA aminoacylation; IBA:GO_Central.
DR CDD; cd00774; GlyRS-like_core; 1.
DR Gene3D; 3.30.930.10; -; 1.
DR Gene3D; 3.40.50.800; -; 1.
DR InterPro; IPR002314; aa-tRNA-synt_IIb.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR004154; Anticodon-bd.
DR InterPro; IPR036621; Anticodon-bd_dom_sf.
DR InterPro; IPR027031; Gly-tRNA_synthase/POLG2.
DR InterPro; IPR033731; GlyRS-like_core.
DR InterPro; IPR002315; tRNA-synt_gly.
DR PANTHER; PTHR10745; PTHR10745; 1.
DR Pfam; PF03129; HGTP_anticodon; 1.
DR Pfam; PF00587; tRNA-synt_2b; 1.
DR PRINTS; PR01043; TRNASYNTHGLY.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00389; glyS_dimeric; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 1: Evidence at protein level;
KW Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase;
KW Nucleotide-binding; Protein biosynthesis; Reference proteome; Transferase.
FT CHAIN 1..618
FT /note="Glycine--tRNA ligase 2"
FT /id="PRO_0000073006"
FT BINDING 187
FT /ligand="glycine"
FT /ligand_id="ChEBI:CHEBI:57305"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 219..221
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 230..231
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 238
FT /ligand="glycine"
FT /ligand_id="ChEBI:CHEBI:57305"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 347..348
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 466..468
FT /ligand="glycine"
FT /ligand_id="ChEBI:CHEBI:57305"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 473
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
SQ SEQUENCE 618 AA; 71018 MW; 91D36F04D1AF7F38 CRC64;
MPLMSNSERD KLESTLRRRF FYTPSFEIYG GVSGLFDLGP PGCQLQNNLI RLWREHFIME
ENMLQVDGPM LTPYDVLKTS GHVDKFTDWM CRNPKTGEYY RADHLIEQTL KKRLLDKDVN
PQDMKNMEKI LTTIDGFSGP ELNLVMQEYN INDPVTNDVL DALTSFNLMF ETKIGASGQL
KAFLRPETAQ GQFLNFNKLL EINQGKIPFA SASIGKSFRN EISPRSGLLR VREFLMAEIE
HFVDPLNKSH AKFNEVLNEE IPLLSRRLQE SGEVQLPVKM TIGEAVNSGM VENETLGYFM
ARVHQFLLNI GINKDKFRFR QHLKNEMAHY ATDCWDGEIL TSYGWIECVG CADRAAFDLT
VHSKKTGRSL TVKQKLDTPK ERTEWVVEVN KKFFGSKFKQ KAKLIESVLS KFSQDELIRR
HEELEKNGEF TCQVNGQIVK LDSSLVTIKM KTTLQHIREY IPNVIEPSFG LGRIIYCIFD
HCFQVRVDSE SRGFFSFPLQ IAPIKVFVTT ISNNDGFPAI LKRISQALRK REIYFKIDDS
NTSIGKKYAR NDELGTPFGI TIDFETIKDQ TVTLRERNSM RQVRGTITDV ISTIDKMLHN
PDESDWDKST FGLSPVKI
