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Glycine--tRNA ligase 1, mitochondrial (EC 6.1.1.14) (Diadenosine tetraphosphate synthetase) (AP-4-A synthetase) (Glycyl-tRNA synthetase 1) (GlyRS 1) (GlyRS1)

 SYG_YEAST               Reviewed;         690 AA.
P38088; D6VQB9;
01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
27-JUL-2011, sequence version 3.
18-JUL-2018, entry version 166.
RecName: Full=Glycine--tRNA ligase 1, mitochondrial;
EC=6.1.1.14;
AltName: Full=Diadenosine tetraphosphate synthetase;
Short=AP-4-A synthetase;
AltName: Full=Glycyl-tRNA synthetase 1;
Short=GlyRS 1;
Short=GlyRS1;
Flags: Precursor;
Name=GRS1; OrderedLocusNames=YBR121C; ORFNames=YBR0917;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=7900426; DOI=10.1002/yea.320101014;
Mannhaupt G., Stucka R., Ehnle S., Vetter I., Feldmann H.;
"Analysis of a 70 kb region on the right arm of yeast chromosome II.";
Yeast 10:1363-1381(1994).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=7813418;
Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J.,
Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C.,
Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M.,
Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L.,
Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J.,
Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T.,
Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A.,
Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B.,
Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I.,
Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M.,
Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A.,
van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I.,
Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H.,
Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.;
"Complete DNA sequence of yeast chromosome II.";
EMBO J. 13:5795-5809(1994).
[3]
GENOME REANNOTATION, AND SEQUENCE REVISION TO 586-587.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=10874035; DOI=10.1074/jbc.M003416200;
Turner R.J., Lovato M., Schimmel P.;
"One of two genes encoding glycyl-tRNA synthetase in Saccharomyces
cerevisiae provides mitochondrial and cytoplasmic functions.";
J. Biol. Chem. 275:27681-27688(2000).
[5]
IDENTIFICATION BY MASS SPECTROMETRY.
PubMed=14690591; DOI=10.1016/S1097-2765(03)00476-3;
Hazbun T.R., Malmstroem L., Anderson S., Graczyk B.J., Fox B.,
Riffle M., Sundin B.A., Aranda J.D., McDonald W.H., Chiu C.-H.,
Snydsman B.E., Bradley P., Muller E.G.D., Fields S., Baker D.,
Yates J.R. III, Davis T.N.;
"Assigning function to yeast proteins by integration of
technologies.";
Mol. Cell 12:1353-1365(2003).
[6]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[7]
ALTERNATIVE INITIATION.
PubMed=14734560; DOI=10.1074/jbc.M311269200;
Chang K.J., Wang C.C.;
"Translation initiation from a naturally occurring non-AUG codon in
Saccharomyces cerevisiae.";
J. Biol. Chem. 279:13778-13785(2004).
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=YAL6B;
PubMed=15665377; DOI=10.1074/mcp.M400219-MCP200;
Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J.,
Mann M., Jensen O.N.;
"Quantitative phosphoproteomics applied to the yeast pheromone
signaling pathway.";
Mol. Cell. Proteomics 4:310-327(2005).
[9]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
[10]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226; SER-476 AND
SER-528, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226; SER-476 AND
THR-689, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
[12]
ACETYLATION [LARGE SCALE ANALYSIS] AT SER-25, CLEAVAGE OF TRANSIT
PEPTIDE [LARGE SCALE ANALYSIS] AFTER MET-24, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22814378; DOI=10.1073/pnas.1210303109;
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E.,
Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K.,
Aldabe R.;
"N-terminal acetylome analyses and functional insights of the N-
terminal acetyltransferase NatB.";
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
-!- FUNCTION: Catalyzes the attachment of glycine to tRNA(Gly). Is
also able produce diadenosine tetraphosphate (Ap4A), a universal
pleiotropic signaling molecule needed for cell regulation
pathways, by direct condensation of 2 ATPs (By similarity).
{ECO:0000250, ECO:0000269|PubMed:10874035}.
-!- CATALYTIC ACTIVITY: ATP + glycine + tRNA(Gly) = AMP + diphosphate
+ glycyl-tRNA(Gly).
-!- SUBUNIT: Homodimer.
-!- SUBCELLULAR LOCATION: Isoform Cytoplasmic: Cytoplasm.
-!- SUBCELLULAR LOCATION: Isoform Mitochondrial: Mitochondrion matrix.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative initiation; Named isoforms=2;
Name=Mitochondrial;
IsoId=P38088-1; Sequence=Displayed;
Note=Produced by alternative initiation at an upstream UUG codon
in-frame of the first AUG used for isoform Cytoplasmic.;
Name=Cytoplasmic;
IsoId=P38088-2; Sequence=VSP_041147;
-!- MISCELLANEOUS: Present with 98400 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase
family. {ECO:0000305}.
-!- CAUTION: GRS1, which appears to be a duplication of GRS2, is
necessary and sufficient for both mitochondrial and cytoplasmic
glycyl-tRNA synthetase activities, suggesting that GRS2 may not be
essential. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAA55623.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
Sequence=CAA85078.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
Sequence=DAA07239.2; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; X78993; CAA55623.1; ALT_INIT; Genomic_DNA.
EMBL; Z35990; CAA85078.1; ALT_INIT; Genomic_DNA.
EMBL; BK006936; DAA07239.2; ALT_INIT; Genomic_DNA.
PIR; S48285; S48285.
RefSeq; NP_009679.2; NM_001178469.2. [P38088-2]
ProteinModelPortal; P38088; -.
SMR; P38088; -.
BioGrid; 32823; 160.
DIP; DIP-6526N; -.
IntAct; P38088; 18.
MINT; P38088; -.
STRING; 4932.YBR121C; -.
iPTMnet; P38088; -.
PaxDb; P38088; -.
PRIDE; P38088; -.
EnsemblFungi; YBR121C; YBR121C; YBR121C. [P38088-2]
GeneID; 852418; -.
KEGG; sce:YBR121C; -.
EuPathDB; FungiDB:YBR121C; -.
SGD; S000000325; GRS1.
GeneTree; ENSGT00390000016949; -.
HOGENOM; HOG000242015; -.
InParanoid; P38088; -.
KO; K01880; -.
OMA; EPSYGID; -.
OrthoDB; EOG092C1IOM; -.
BioCyc; YEAST:G3O-29078-MONOMER; -.
BRENDA; 6.1.1.14; 984.
PRO; PR:P38088; -.
Proteomes; UP000002311; Chromosome II.
GO; GO:0005737; C:cytoplasm; IMP:SGD.
GO; GO:0005759; C:mitochondrial matrix; IEA:UniProtKB-SubCell.
GO; GO:0005739; C:mitochondrion; IMP:SGD.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004820; F:glycine-tRNA ligase activity; IDA:SGD.
GO; GO:0046983; F:protein dimerization activity; ISS:UniProtKB.
GO; GO:0015966; P:diadenosine tetraphosphate biosynthetic process; ISS:UniProtKB.
GO; GO:0006353; P:DNA-templated transcription, termination; IMP:SGD.
GO; GO:0006426; P:glycyl-tRNA aminoacylation; IMP:SGD.
GO; GO:0070150; P:mitochondrial glycyl-tRNA aminoacylation; IMP:SGD.
CDD; cd00774; GlyRS-like_core; 1.
Gene3D; 3.40.50.800; -; 1.
InterPro; IPR006195; aa-tRNA-synth_II.
InterPro; IPR004154; Anticodon-bd.
InterPro; IPR036621; Anticodon-bd_dom_sf.
InterPro; IPR027031; Gly-tRNA_synthase/POLG2.
InterPro; IPR033731; GlyRS-like_core.
InterPro; IPR002315; tRNA-synt_gly.
PANTHER; PTHR10745; PTHR10745; 1.
Pfam; PF03129; HGTP_anticodon; 1.
PRINTS; PR01043; TRNASYNTHGLY.
TIGRFAMs; TIGR00389; glyS_dimeric; 1.
PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
1: Evidence at protein level;
Acetylation; Alternative initiation; Aminoacyl-tRNA synthetase;
ATP-binding; Complete proteome; Cytoplasm; Ligase; Mitochondrion;
Nucleotide-binding; Phosphoprotein; Protein biosynthesis;
Reference proteome; Transit peptide.
TRANSIT 1 24 Mitochondrion.
{ECO:0000244|PubMed:22814378,
ECO:0000255}.
CHAIN 25 690 Glycine--tRNA ligase 1, mitochondrial.
/FTId=PRO_0000073005.
NP_BIND 283 285 ATP. {ECO:0000250}.
NP_BIND 293 298 ATP. {ECO:0000250}.
NP_BIND 410 411 ATP. {ECO:0000250}.
NP_BIND 535 538 ATP. {ECO:0000250}.
REGION 298 302 Substrate binding. {ECO:0000250}.
REGION 531 535 Substrate binding. {ECO:0000250}.
BINDING 132 132 Substrate. {ECO:0000250}.
BINDING 251 251 Substrate. {ECO:0000250}.
BINDING 388 388 Substrate. {ECO:0000250}.
BINDING 388 388 Substrate; via carbonyl oxygen.
{ECO:0000250}.
MOD_RES 25 25 N-acetylserine.
{ECO:0000244|PubMed:22814378}.
MOD_RES 226 226 Phosphoserine.
{ECO:0000244|PubMed:15665377,
ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
MOD_RES 476 476 Phosphoserine.
{ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
MOD_RES 528 528 Phosphoserine.
{ECO:0000244|PubMed:18407956}.
MOD_RES 689 689 Phosphothreonine.
{ECO:0000244|PubMed:19779198}.
VAR_SEQ 1 23 Missing (in isoform Cytoplasmic).
/FTId=VSP_041147.
CONFLICT 586 587 TT -> HH (in Ref. 1; CAA55623 and 2;
CAA85078). {ECO:0000305}.
SEQUENCE 690 AA; 78184 MW; 4EBDE6F0A942F7F6 CRC64;
MSFFNISRRF YSQIVKKSVK IKRMSVEDIK KARAAVPFNR EQLESVLRGR FFYAPAFDLY
GGVSGLYDYG PPGCAFQNNI IDAWRKHFIL EEDMLEVDCT MLTPYEVLKT SGHVDKFSDW
MCRDLKTGEI FRADHLVEEV LEARLKGDQE ARGLVEDANA AAKDDAEKKK RKKKVKQIKA
VKLDDDVVKE YEEILAKIDG YSGPELGELM EKYDIGNPVT GETLESPRAF NLMFETAIGP
SGQLKGYLRP ETAQGQFLNF NKLLEFNNSK TPFASASIGK SFRNEISPRA GLLRVREFLM
AEIEHFVDPL DKSHPKFNEI KDIKLSFLPR DVQEAGSTEP IVKTVGEAVA SRMVDNETLG
YFIARIYQFL MKIGVDESKL RFRQHMANEM AHYAADCWDG ELKTSYGWIE CVGCADRSAY
DLTVHSKKTK EKLVVRQKLD NPIEVTKWEI DLTKKLFGPK FRKDAPKVES HLLNMSQDDL
ASKAELLKAN GKFTIKVDGV DGEVELDDKL VKIEQRTKVE HVREYVPSVI EPSFGIGRII
YSVFEHSFWN RPEDNARSVL SFPPLVAPTK VLLVPLSNHK DLVPVTTEVA KILRKSQIPF
KIDDSGVSIG KRYARNDELG TPFGVTIDFE SAKDHSVTLR ERDSTKQVRG SVENVIKAIR
DITYNGASWE EGTKDLTPFI AQAEAEAETD


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