SYGM1_ARATH
ID SYGM1_ARATH Reviewed; 729 AA.
AC O23627; Q8LBY0; Q949T7;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 165.
DE RecName: Full=Glycine--tRNA ligase, mitochondrial 1 {ECO:0000305};
DE EC=6.1.1.14 {ECO:0000269|PubMed:11278923};
DE AltName: Full=Diadenosine tetraphosphate synthetase {ECO:0000305};
DE Short=Ap4A synthetase {ECO:0000305};
DE EC=2.7.7.- {ECO:0000250|UniProtKB:P41250};
DE AltName: Full=Glycyl-tRNA synthetase 1 {ECO:0000303|PubMed:11278923};
DE Short=GlyRS-1 {ECO:0000303|PubMed:11278923};
DE Flags: Precursor;
GN OrderedLocusNames=At1g29880; ORFNames=F1N18.8;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Columbia;
RA Duchene A.-M., Dietrich A.;
RT "Isolation and characterization of a glycyl-tRNA synthetase sequence from
RT Arabidopsis thaliana.";
RL (er) Plant Gene Register PGR97-183(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP CATALYTIC ACTIVITY, AND SUBCELLULAR LOCATION.
RX PubMed=11278923; DOI=10.1074/jbc.m011525200;
RA Duchene A.-M., Peeters N., Dietrich A., Cosset A., Small I.D., Wintz H.;
RT "Overlapping destinations for two dual targeted glycyl-tRNA synthetases in
RT Arabidopsis thaliana and Phaseolus vulgaris.";
RL J. Biol. Chem. 276:15275-15283(2001).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1 (ISOFORM CYTOPLASMIC), AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
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). Also produces diadenosine tetraphosphate
CC (Ap4A), a universal pleiotropic signaling molecule needed for cell
CC regulation pathways, by direct condensation of 2 ATPs. Thereby, may
CC play a special role in Ap4A homeostasis.
CC {ECO:0000250|UniProtKB:P41250}.
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:11278923};
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 -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:P41250}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:11278923}.
CC Cytoplasm, cytosol {ECO:0000269|PubMed:11278923}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative initiation; Named isoforms=2;
CC Name=Mitochondrial;
CC IsoId=O23627-1; Sequence=Displayed;
CC Name=Cytoplasmic;
CC IsoId=O23627-2; Sequence=VSP_018906;
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM64494.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AJ002062; CAA05162.1; -; mRNA.
DR EMBL; AC008030; AAG10608.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31145.1; -; Genomic_DNA.
DR EMBL; AY050895; AAK92832.1; -; mRNA.
DR EMBL; AY086930; AAM64494.1; ALT_INIT; mRNA.
DR PIR; D86422; D86422.
DR RefSeq; NP_564337.1; NM_102728.3. [O23627-1]
DR AlphaFoldDB; O23627; -.
DR SMR; O23627; -.
DR BioGRID; 25101; 11.
DR STRING; 3702.AT1G29880.1; -.
DR iPTMnet; O23627; -.
DR MetOSite; O23627; -.
DR SwissPalm; O23627; -.
DR PaxDb; O23627; -.
DR PRIDE; O23627; -.
DR ProteomicsDB; 233040; -. [O23627-1]
DR EnsemblPlants; AT1G29880.1; AT1G29880.1; AT1G29880. [O23627-1]
DR GeneID; 839866; -.
DR Gramene; AT1G29880.1; AT1G29880.1; AT1G29880. [O23627-1]
DR KEGG; ath:AT1G29880; -.
DR Araport; AT1G29880; -.
DR TAIR; locus:2019327; AT1G29880.
DR eggNOG; KOG2298; Eukaryota.
DR HOGENOM; CLU_015515_1_0_1; -.
DR InParanoid; O23627; -.
DR OMA; NDGFPAI; -.
DR OrthoDB; 1183820at2759; -.
DR PhylomeDB; O23627; -.
DR BRENDA; 6.1.1.14; 399.
DR PRO; PR:O23627; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; O23627; baseline and differential.
DR Genevisible; O23627; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0005768; C:endosome; HDA:TAIR.
DR GO; GO:0005794; C:Golgi apparatus; HDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0005802; C:trans-Golgi network; HDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004820; F:glycine-tRNA ligase activity; ISS:UniProtKB.
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; IBA:GO_Central.
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; IPR009068; S15_NS1_RNA-bd.
DR InterPro; IPR002315; tRNA-synt_gly.
DR InterPro; IPR000738; WHEP-TRS_dom.
DR PANTHER; PTHR10745; PTHR10745; 1.
DR Pfam; PF03129; HGTP_anticodon; 1.
DR Pfam; PF00587; tRNA-synt_2b; 1.
DR Pfam; PF00458; WHEP-TRS; 1.
DR PRINTS; PR01043; TRNASYNTHGLY.
DR SMART; SM00991; WHEP-TRS; 1.
DR SUPFAM; SSF47060; SSF47060; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00389; glyS_dimeric; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
DR PROSITE; PS00762; WHEP_TRS_1; 1.
DR PROSITE; PS51185; WHEP_TRS_2; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative initiation; Aminoacyl-tRNA synthetase;
KW ATP-binding; Cytoplasm; Ligase; Mitochondrion; Nucleotide-binding;
KW Protein biosynthesis; Reference proteome; Transferase; Transit peptide.
FT TRANSIT 1..28
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 29..729
FT /note="Glycine--tRNA ligase, mitochondrial 1"
FT /id="PRO_0000035802"
FT DOMAIN 50..106
FT /note="WHEP-TRS"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00531"
FT BINDING 296
FT /ligand="glycine"
FT /ligand_id="ChEBI:CHEBI:57305"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 328..330
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 339..340
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 347
FT /ligand="glycine"
FT /ligand_id="ChEBI:CHEBI:57305"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 454..455
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 575..577
FT /ligand="glycine"
FT /ligand_id="ChEBI:CHEBI:57305"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 582
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT VAR_SEQ 1..39
FT /note="Missing (in isoform Cytoplasmic)"
FT /evidence="ECO:0000305"
FT /id="VSP_018906"
FT CONFLICT 1
FT /note="M -> T (in Ref. 5; AAM64494)"
FT /evidence="ECO:0000305"
FT CONFLICT 82
FT /note="I -> M (in Ref. 4; AAK92832)"
FT /evidence="ECO:0000305"
FT CONFLICT 632
FT /note="V -> A (in Ref. 5; AAM64494)"
FT /evidence="ECO:0000305"
FT MOD_RES O23627-2:1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
SQ SEQUENCE 729 AA; 81944 MW; BFF40B27571794E6 CRC64;
MRIFSTFVFH RRQQIFNLRQ FQTTTILRNP ISIAPIQIPM DATEQSLRQS LSEKSSSVEA
QGNAVRALKA SRAAKPEIDA AIEQLNKLKL EKSTVEKELQ SIISSSGNGS LNREAFRKAV
VNTLERRLFY IPSFKIYSGV AGLFDYGPPG CAIKSNVLSF WRQHFILEEN MLEVDCPCVT
PEVVLKASGH VDKFTDLMVK DEKTGTCYRA DHLLKDYCTE KLEKDLTISA EKAAELKDVL
AVMEDFSPEQ LGAKIREYGI TAPDTKNPLS DPYPFNLMFQ TSIGPSGLIP GYMRPETAQG
IFVNFKDLYY YNGKKLPFAA AQIGQAFRNE ISPRQGLLRV REFTLAEIEH FVDPENKSHP
KFSDVAKLEF LMFPREEQMS GQSAKKLCLG EAVAKGTVNN ETLGYFIGRV YLFLTRLGID
KERLRFRQHL ANEMAHYAAD CWDAEIESSY GWIECVGIAD RSAYDLRAHS DKSGTPLVAE
EKFAEPKEVE KLVITPVKKE LGLAFKGNQK NVVESLEAMN EEEAMEMKAT LESKGEVEFY
VCTLKKSVNI KKNMVSISKE KKKEHQRVFT PSVIEPSFGI GRIIYCLYEH CFSTRPSKAG
DEQLNLFRFP PLVAPIKCTV FPLVQNQQFE EVAKVISKEL ASVGISHKID ITGTSIGKRY
ARTDELGVPF AITVDSDTSV TIRERDSKDQ VRVTLKEAAS VVSSVSEGKM TWQDVWATFP
HHSSAAADE
