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P38088 (SYG_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 130. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Glycine--tRNA ligase 1, mitochondrial

EC=6.1.1.14
Alternative name(s):
Diadenosine tetraphosphate synthetase
Short name=AP-4-A synthetase
Glycyl-tRNA synthetase 1
Short name=GlyRS 1
Short name=GlyRS1
Gene names
Name:GRS1
Ordered Locus Names:YBR121C
ORF Names:YBR0917
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length690 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.4

Catalytic activity

ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly).

Subunit structure

Homodimer.

Subcellular location

Isoform Cytoplasmic: Cytoplasm Ref.4.

Isoform Mitochondrial: Mitochondrion matrix Ref.4.

Miscellaneous

Present with 98400 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the class-II aminoacyl-tRNA synthetase family.

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.

Sequence caution

The sequence CAA55623.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence CAA85078.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence DAA07239.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Alternative products

This entry describes 2 isoforms produced by alternative initiation. [Align] [Select]
Isoform Mitochondrial (identifier: P38088-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Note: Produced by alternative initiation at an upstream UUG codon in-frame of the first AUG used for isoform Cytoplasmic.
Isoform Cytoplasmic (identifier: P38088-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-23: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 2424Mitochondrion Potential
Chain25 – 690666Glycine--tRNA ligase 1, mitochondrial
PRO_0000073005

Regions

Nucleotide binding283 – 2853ATP By similarity
Nucleotide binding293 – 2986ATP By similarity
Nucleotide binding410 – 4112ATP By similarity
Nucleotide binding535 – 5384ATP By similarity
Region298 – 3025Substrate binding By similarity
Region531 – 5355Substrate binding By similarity

Sites

Binding site1321Substrate By similarity
Binding site2511Substrate By similarity
Binding site3881Substrate By similarity
Binding site3881Substrate; via carbonyl oxygen By similarity

Amino acid modifications

Modified residue251N-acetylserine Ref.11
Modified residue2261Phosphoserine Ref.7 Ref.8 Ref.9 Ref.10
Modified residue4761Phosphoserine Ref.9 Ref.10
Modified residue5281Phosphoserine Ref.9
Modified residue6891Phosphothreonine Ref.10

Natural variations

Alternative sequence1 – 2323Missing in isoform Cytoplasmic.
VSP_041147

Experimental info

Sequence conflict586 – 5872TT → HH in CAA55623. Ref.1
Sequence conflict586 – 5872TT → HH in CAA85078. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform Mitochondrial [UniParc].

Last modified July 27, 2011. Version 3.
Checksum: 4EBDE6F0A942F7F6

FASTA69078,184
        10         20         30         40         50         60 
MSFFNISRRF YSQIVKKSVK IKRMSVEDIK KARAAVPFNR EQLESVLRGR FFYAPAFDLY 

        70         80         90        100        110        120 
GGVSGLYDYG PPGCAFQNNI IDAWRKHFIL EEDMLEVDCT MLTPYEVLKT SGHVDKFSDW 

       130        140        150        160        170        180 
MCRDLKTGEI FRADHLVEEV LEARLKGDQE ARGLVEDANA AAKDDAEKKK RKKKVKQIKA 

       190        200        210        220        230        240 
VKLDDDVVKE YEEILAKIDG YSGPELGELM EKYDIGNPVT GETLESPRAF NLMFETAIGP 

       250        260        270        280        290        300 
SGQLKGYLRP ETAQGQFLNF NKLLEFNNSK TPFASASIGK SFRNEISPRA GLLRVREFLM 

       310        320        330        340        350        360 
AEIEHFVDPL DKSHPKFNEI KDIKLSFLPR DVQEAGSTEP IVKTVGEAVA SRMVDNETLG 

       370        380        390        400        410        420 
YFIARIYQFL MKIGVDESKL RFRQHMANEM AHYAADCWDG ELKTSYGWIE CVGCADRSAY 

       430        440        450        460        470        480 
DLTVHSKKTK EKLVVRQKLD NPIEVTKWEI DLTKKLFGPK FRKDAPKVES HLLNMSQDDL 

       490        500        510        520        530        540 
ASKAELLKAN GKFTIKVDGV DGEVELDDKL VKIEQRTKVE HVREYVPSVI EPSFGIGRII 

       550        560        570        580        590        600 
YSVFEHSFWN RPEDNARSVL SFPPLVAPTK VLLVPLSNHK DLVPVTTEVA KILRKSQIPF 

       610        620        630        640        650        660 
KIDDSGVSIG KRYARNDELG TPFGVTIDFE SAKDHSVTLR ERDSTKQVRG SVENVIKAIR 

       670        680        690 
DITYNGASWE EGTKDLTPFI AQAEAEAETD 

« Hide

Isoform Cytoplasmic [UniParc].

Checksum: B62E3DDAD7E87552
Show »

FASTA66775,339

References

« Hide 'large scale' references
[1]"Analysis of a 70 kb region on the right arm of yeast chromosome II."
Mannhaupt G., Stucka R., Ehnle S., Vetter I., Feldmann H.
Yeast 10:1363-1381(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[2]"Complete DNA sequence of yeast chromosome II."
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. expand/collapse author list , 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.
EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
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.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 586-587.
Strain: ATCC 204508 / S288c.
[4]"One of two genes encoding glycyl-tRNA synthetase in Saccharomyces cerevisiae provides mitochondrial and cytoplasmic functions."
Turner R.J., Lovato M., Schimmel P.
J. Biol. Chem. 275:27681-27688(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
[5]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[6]"Translation initiation from a naturally occurring non-AUG codon in Saccharomyces cerevisiae."
Chang K.J., Wang C.C.
J. Biol. Chem. 279:13778-13785(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: ALTERNATIVE INITIATION.
[7]"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway."
Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N.
Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Strain: YAL6B.
[8]"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Strain: ADR376.
[9]"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226; SER-476 AND SER-528, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226; SER-476 AND THR-689, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
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.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-25, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X78993 Genomic DNA. Translation: CAA55623.1. Different initiation.
Z35990 Genomic DNA. Translation: CAA85078.1. Different initiation.
BK006936 Genomic DNA. Translation: DAA07239.2. Different initiation.
PIRS48285.
RefSeqNP_009679.2. NM_001178469.2. [P38088-2]

3D structure databases

ProteinModelPortalP38088.
SMRP38088. Positions 39-437, 521-671.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32823. 41 interactions.
DIPDIP-6526N.
IntActP38088. 13 interactions.
MINTMINT-690383.
STRING4932.YBR121C.

Proteomic databases

MaxQBP38088.
PaxDbP38088.
PeptideAtlasP38088.
PRIDEP38088.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID852418.
KEGGsce:YBR121C.

Organism-specific databases

CYGDYBR121c.
SGDS000000325. GRS1.

Phylogenomic databases

eggNOGCOG0423.
HOGENOMHOG000242015.
KOK01880.
OMALMFQTTI.
OrthoDBEOG76TB17.

Enzyme and pathway databases

BioCycYEAST:G3O-29078-MONOMER.

Gene expression databases

GenevestigatorP38088.

Family and domain databases

Gene3D3.40.50.800. 1 hit.
InterProIPR002314. aa-tRNA-synt_IIb_cons-dom.
IPR006195. aa-tRNA-synth_II.
IPR004154. Anticodon-bd.
IPR027031. Gly-tRNA_synthase/POLG2.
IPR002315. tRNA-synt_gly.
[Graphical view]
PANTHERPTHR10745. PTHR10745. 1 hit.
PfamPF03129. HGTP_anticodon. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
[Graphical view]
PRINTSPR01043. TRNASYNTHGLY.
SUPFAMSSF52954. SSF52954. 1 hit.
TIGRFAMsTIGR00389. glyS_dimeric. 1 hit.
PROSITEPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio971279.

Entry information

Entry nameSYG_YEAST
AccessionPrimary (citable) accession number: P38088
Secondary accession number(s): D6VQB9
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: July 27, 2011
Last modified: June 11, 2014
This is version 130 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome II

Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries