SYGM2_ARATH
ID SYGM2_ARATH Reviewed; 1067 AA.
AC Q8L785; O23150; Q9SU73;
DT 07-FEB-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Glycine--tRNA ligase, chloroplastic/mitochondrial 2 {ECO:0000305};
DE EC=6.1.1.14 {ECO:0000269|PubMed:11278923};
DE AltName: Full=Glycyl-tRNA synthetase 2 {ECO:0000303|PubMed:11278923};
DE Short=GlyRS-2 {ECO:0000303|PubMed:11278923};
DE AltName: Full=Protein EMBRYO-DEFECTIVE-DEVELOPMENT 1 {ECO:0000303|PubMed:9707529};
DE Flags: Precursor;
GN Name=EDD1 {ECO:0000303|PubMed:9707529}; OrderedLocusNames=At3g48110;
GN ORFNames=T17F15.20;
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] (ISOFORM 1), AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. C24; TISSUE=Flower bud, and Silique;
RX PubMed=9707529; DOI=10.2307/3870640;
RA Uwer U., Altmann T., Willmitzer L.;
RT "Inactivation of a glycyl-tRNA synthetase leads to an arrest in plant
RT embryo development.";
RL Plant Cell 10:1277-1294(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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] (ISOFORM 1).
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] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Cheuk R.F., Chen H., Kim C.J., Shinn P., Carninci P., Hayashizaki Y.,
RA Ishida J., Kamiya A., Kawai J., Narusaka M., Sakurai T., Satou M., Seki M.,
RA Shinozaki K., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAR-2004) 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 DISRUPTION PHENOTYPE.
RX PubMed=22791832; DOI=10.1093/jxb/ers184;
RA Moschopoulos A., Derbyshire P., Byrne M.E.;
RT "The Arabidopsis organelle-localized glycyl-tRNA synthetase encoded by
RT EMBRYO DEFECTIVE DEVELOPMENT1 is required for organ patterning.";
RL J. Exp. Bot. 63:5233-5243(2012).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE AFTER
RP ALA-50.
RX PubMed=25732537; DOI=10.1093/jxb/erv064;
RA Carrie C., Venne A.S., Zahedi R.P., Soll J.;
RT "Identification of cleavage sites and substrate proteins for two
RT mitochondrial intermediate peptidases in Arabidopsis thaliana.";
RL J. Exp. Bot. 66:2691-2708(2015).
CC -!- FUNCTION: Catalyzes the attachment of glycine to tRNA(Gly). Is also
CC able produce diadenosine tetraphosphate (Ap4A), a universal pleiotropic
CC signaling molecule needed for cell regulation pathways, by direct
CC condensation of 2 ATPs. {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 -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:P41250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:11278923}. Mitochondrion
CC {ECO:0000269|PubMed:11278923, ECO:0000305|PubMed:25732537}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8L785-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8L785-2; Sequence=VSP_018098;
CC -!- DISRUPTION PHENOTYPE: Embryo defective. Developmental arrest of the
CC embryo between the globular and heart stages (PubMed:9707529). Plants
CC with partial loss of EDD1 display changes in patterning of margin and
CC distal regions of leaves (PubMed:22791832).
CC {ECO:0000269|PubMed:22791832, ECO:0000269|PubMed:9707529}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing donor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB41128.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AJ003069; CAA05843.1; -; mRNA.
DR EMBL; AL049658; CAB41128.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE78369.1; -; Genomic_DNA.
DR EMBL; AY136413; AAM97079.1; -; mRNA.
DR EMBL; BT012191; AAS76678.1; -; mRNA.
DR PIR; T06672; T06672.
DR PIR; T48850; T48850.
DR RefSeq; NP_190394.3; NM_114680.4. [Q8L785-1]
DR AlphaFoldDB; Q8L785; -.
DR SMR; Q8L785; -.
DR STRING; 3702.AT3G48110.1; -.
DR iPTMnet; Q8L785; -.
DR PaxDb; Q8L785; -.
DR PRIDE; Q8L785; -.
DR ProteomicsDB; 233021; -. [Q8L785-1]
DR EnsemblPlants; AT3G48110.1; AT3G48110.1; AT3G48110. [Q8L785-1]
DR GeneID; 823966; -.
DR Gramene; AT3G48110.1; AT3G48110.1; AT3G48110. [Q8L785-1]
DR KEGG; ath:AT3G48110; -.
DR Araport; AT3G48110; -.
DR TAIR; locus:2097885; AT3G48110.
DR eggNOG; ENOG502QS5T; Eukaryota.
DR HOGENOM; CLU_007220_0_0_1; -.
DR InParanoid; Q8L785; -.
DR OMA; LPIPKRM; -.
DR OrthoDB; 903183at2759; -.
DR PhylomeDB; Q8L785; -.
DR BRENDA; 6.1.1.14; 399.
DR PRO; PR:Q8L785; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q8L785; baseline and differential.
DR Genevisible; Q8L785; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IDA: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:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0006426; P:glycyl-tRNA aminoacylation; ISS:TAIR.
DR GO; GO:0045995; P:regulation of embryonic development; IMP:TAIR.
DR CDD; cd00733; GlyRS_alpha_core; 1.
DR Gene3D; 3.30.930.10; -; 1.
DR HAMAP; MF_00254; Gly_tRNA_synth_alpha; 1.
DR HAMAP; MF_00255; Gly_tRNA_synth_beta; 1.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR015944; Gly-tRNA-synth_bsu.
DR InterPro; IPR006194; Gly-tRNA-synth_heterodimer.
DR InterPro; IPR002310; Gly-tRNA_ligase_asu.
DR PANTHER; PTHR30075; PTHR30075; 1.
DR Pfam; PF02091; tRNA-synt_2e; 1.
DR Pfam; PF02092; tRNA_synt_2f; 1.
DR PRINTS; PR01044; TRNASYNTHGA.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00388; glyQ; 1.
DR TIGRFAMs; TIGR00211; glyS; 1.
DR PROSITE; PS50861; AA_TRNA_LIGASE_II_GLYAB; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; Aminoacyl-tRNA synthetase; ATP-binding; Chloroplast;
KW Ligase; Mitochondrion; Nucleotide-binding; Plastid; Protein biosynthesis;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..50
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000269|PubMed:25732537"
FT CHAIN 51..1067
FT /note="Glycine--tRNA ligase, chloroplastic/mitochondrial 2"
FT /evidence="ECO:0000305"
FT /id="PRO_0000046017"
FT BINDING 513
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 589..596
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 619..624
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 624..628
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 744..745
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 855..859
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT BINDING 859..862
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P41250"
FT VAR_SEQ 1035
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_018098"
FT CONFLICT 336
FT /note="S -> T (in Ref. 1; CAA05843)"
FT /evidence="ECO:0000305"
FT CONFLICT 535
FT /note="M -> I (in Ref. 1; CAA05843)"
FT /evidence="ECO:0000305"
FT CONFLICT 616
FT /note="S -> N (in Ref. 1; CAA05843)"
FT /evidence="ECO:0000305"
FT CONFLICT 893
FT /note="T -> R (in Ref. 1; CAA05843)"
FT /evidence="ECO:0000305"
FT CONFLICT 1012
FT /note="D -> E (in Ref. 1; CAA05843)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1067 AA; 119773 MW; E2F0574F1F019493 CRC64;
MAILHFSLPL IVSFLRPHAS PRFFLLPRSL SQSPFLSRRR FHRTSAVSSA AVHHQSYRNP
DDDVTRAVSV PTFQQAIQRL QEYWASVGCA VMQPSNTEVG AGTMNPCTFL RVLGPEPWNV
AYVEPSIRPD DSRYGENPNR LQRHTQFQVI LKPDPGNSQQ LFINSLSALG IDVTAHDIRF
VEDNWESPVL GAWGLGWEIW MDGMEITQFT YFQQAGSLPL SPVSVEITYG LERIIMLLQE
VDHFKKILYA DGITYGELFL ENEKEMSSYY LEHASVDRLQ KHFDYFDEEA RSLLALGLPI
PAYDQLLKTS HAFNILDARG FIGVTERARY FGRMRSLARQ CAQLWLATRE SLGHPLGVAS
EPVPPVCHRA ALEKVAEKVS EDPRSFIIEI GTEEMPPQDV INASEQLRVL VLELLENQRL
RHGAVKAFGT PRRLVVLVDA MSSKQLEEEV EVRGPPASKA FDDEGNPTKA AEGFSRRYGV
PLEKLYRKVS GKTEYVHARV TEPARLALEV LSEDLPGILA KISFPKSMRW NSSVMFSRPI
RWVMALHGDL VVPFSFAGIS SGNVSCGLRN TASASLLVQN AESYEDTMRN SGINIEIEER
KKIILEKSNA LAKSVSGRLV VPQNLLNEVA NLVEAPVPLI GKFKESFLEL PEELLTIVMQ
KHQKYFSIID ESGQLLPYFI AVANGAINED VVKKGNEAVL RARYEDAKFF YEVDTRKRFS
EFRDQLQGIL FHEKLGTMLD KMNRLKKMVS KLCLALKIDE DLLPVVEDAA SLAMSDLATA
VVTEFTALSG IMARHYALRD GYSEQIAEAL LEITLPRFSG DVIPKTDAGM VLAIGDRLDS
LVGLFAAGCQ PSSTNDPFGL RRISYGLVQI LVEKDKNVNF KRVLELAASV QPTKVEANTV
EDVYQFVTRR LEQLLVDNGV SPEVVRSVLA ERGNNPCLAA RTAYKTEKLS KGEMFPKIVE
AYSRPTRIVR GKDVGVGVEV DENAFETPQE RTLWSTYTSI KDRIHTGIEI EDFTEISMQL
VEPLEDFFNN VFVMVEEERV RKNRLALLNN IANLPKGVID LSFLPGF
