Reviewed, UniProtKB/Swiss-Prot O23627 (SYGM1_ARATH)

Names and origin

Protein names

Recommended name:
    Glycyl-tRNA synthetase 1, mitochondrial
    EC=6.1.1.14
Alternative name(s):
    Glycine--tRNA ligase 1
      Short name=GlyRS 1
    Diadenosine tetraphosphate synthetase
      Short name=AP-4-A synthetase

Gene names

Name:	GLYRS-1
Ordered Locus Names:	At1g29880
ORF Names:	F1N18.8

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	729 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at transcript 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.
Catalytic activity	ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly).
Subunit structure	Homodimer By similarity.
Subcellular location	Mitochondrion. Cytoplasm Ref.5.
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family. Contains 1 WHEP-TRS domain.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm Mitochondrion
Coding sequence diversity	Alternative initiation
Domain	Transit peptide
Ligand	ATP-binding Nucleotide-binding
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	diadenosine tetraphosphate biosynthetic process Inferred from sequence or structural similarity. Source: UniProtKB glycyl-tRNA aminoacylation Inferred from electronic annotation. Source: InterPro response to cadmium ion Inferred from expression pattern. Source: TAIR
Cellular component	mitochondrion Inferred from direct assay. Source: TAIR
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW glycine-tRNA ligase activity Inferred from sequence or structural similarity. Source: UniProtKB protein dimerization activity Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative initiation. [Align] [Select]

Isoform Mitochondrial (identifier: O23627-1)

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.

Isoform Cytoplasmic (identifier: O23627-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-39: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 28	28	Mitochondrion Potential
	Chain	29 – 729	701	Glycyl-tRNA synthetase 1, mitochondrial		PRO_0000035802
Regions
	Domain	50 – 106	57	WHEP-TRS
	Nucleotide binding	328 – 330	3	ATP By similarity
	Nucleotide binding	338 – 343	6	ATP By similarity
	Nucleotide binding	454 – 455	2	ATP By similarity
	Nucleotide binding	579 – 582	4	ATP By similarity
	Region	343 – 347	5	Substrate binding By similarity
	Region	575 – 579	5	Substrate binding By similarity
Sites
	Binding site	209	1	Substrate By similarity
	Binding site	296	1	Substrate By similarity
	Binding site	432	1	Substrate By similarity
	Binding site	432	1	Substrate; via carbonyl oxygen By similarity
Natural variations
	Alternative sequence	1 – 39	39	Missing in isoform Cytoplasmic.		VSP_018906
Experimental info
	Sequence conflict	1	1	M → T Ref.4
	Sequence conflict	82	1	I → M in AAK92832. Ref.3
	Sequence conflict	632	1	V → A in AAM64494. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	Isoform Mitochondrial [UniParc]. Last modified January 1, 1998. Version 1. Checksum: BFF40B27571794E6	FASTA	729	81,944
	10 20 30 40 50 60 MRIFSTFVFH RRQQIFNLRQ FQTTTILRNP ISIAPIQIPM DATEQSLRQS LSEKSSSVEA 70 80 90 100 110 120 QGNAVRALKA SRAAKPEIDA AIEQLNKLKL EKSTVEKELQ SIISSSGNGS LNREAFRKAV 130 140 150 160 170 180 VNTLERRLFY IPSFKIYSGV AGLFDYGPPG CAIKSNVLSF WRQHFILEEN MLEVDCPCVT 190 200 210 220 230 240 PEVVLKASGH VDKFTDLMVK DEKTGTCYRA DHLLKDYCTE KLEKDLTISA EKAAELKDVL 250 260 270 280 290 300 AVMEDFSPEQ LGAKIREYGI TAPDTKNPLS DPYPFNLMFQ TSIGPSGLIP GYMRPETAQG 310 320 330 340 350 360 IFVNFKDLYY YNGKKLPFAA AQIGQAFRNE ISPRQGLLRV REFTLAEIEH FVDPENKSHP 370 380 390 400 410 420 KFSDVAKLEF LMFPREEQMS GQSAKKLCLG EAVAKGTVNN ETLGYFIGRV YLFLTRLGID 430 440 450 460 470 480 KERLRFRQHL ANEMAHYAAD CWDAEIESSY GWIECVGIAD RSAYDLRAHS DKSGTPLVAE 490 500 510 520 530 540 EKFAEPKEVE KLVITPVKKE LGLAFKGNQK NVVESLEAMN EEEAMEMKAT LESKGEVEFY 550 560 570 580 590 600 VCTLKKSVNI KKNMVSISKE KKKEHQRVFT PSVIEPSFGI GRIIYCLYEH CFSTRPSKAG 610 620 630 640 650 660 DEQLNLFRFP PLVAPIKCTV FPLVQNQQFE EVAKVISKEL ASVGISHKID ITGTSIGKRY 670 680 690 700 710 720 ARTDELGVPF AITVDSDTSV TIRERDSKDQ VRVTLKEAAS VVSSVSEGKM TWQDVWATFP HHSSAAADE
	Isoform Cytoplasmic. Checksum: 705B4179AF455F3E	FASTA	690	77,231
	10 20 30 40 50 60 MDATEQSLRQ SLSEKSSSVE AQGNAVRALK ASRAAKPEID AAIEQLNKLK LEKSTVEKEL 70 80 90 100 110 120 QSIISSSGNG SLNREAFRKA VVNTLERRLF YIPSFKIYSG VAGLFDYGPP GCAIKSNVLS 130 140 150 160 170 180 FWRQHFILEE NMLEVDCPCV TPEVVLKASG HVDKFTDLMV KDEKTGTCYR ADHLLKDYCT 190 200 210 220 230 240 EKLEKDLTIS AEKAAELKDV LAVMEDFSPE QLGAKIREYG ITAPDTKNPL SDPYPFNLMF 250 260 270 280 290 300 QTSIGPSGLI PGYMRPETAQ GIFVNFKDLY YYNGKKLPFA AAQIGQAFRN EISPRQGLLR 310 320 330 340 350 360 VREFTLAEIE HFVDPENKSH PKFSDVAKLE FLMFPREEQM SGQSAKKLCL GEAVAKGTVN 370 380 390 400 410 420 NETLGYFIGR VYLFLTRLGI DKERLRFRQH LANEMAHYAA DCWDAEIESS YGWIECVGIA 430 440 450 460 470 480 DRSAYDLRAH SDKSGTPLVA EEKFAEPKEV EKLVITPVKK ELGLAFKGNQ KNVVESLEAM 490 500 510 520 530 540 NEEEAMEMKA TLESKGEVEF YVCTLKKSVN IKKNMVSISK EKKKEHQRVF TPSVIEPSFG 550 560 570 580 590 600 IGRIIYCLYE HCFSTRPSKA GDEQLNLFRF PPLVAPIKCT VFPLVQNQQF EEVAKVISKE 610 620 630 640 650 660 LASVGISHKI DITGTSIGKR YARTDELGVP FAITVDSDTS VTIRERDSKD QVRVTLKEAA 670 680 690 SVVSSVSEGK MTWQDVWATF PHHSSAAADE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Isolation and characterization of a glycyl-tRNA synthetase sequence from Arabidopsis thaliana." Duchene A.-M., Dietrich A. Plant Gene Register PGR97-183 Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Columbia.
[2]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed: 11130712] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[4]	"Full-length cDNA from Arabidopsis thaliana." Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A. Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[5]	"Overlapping destinations for two dual targeted glycyl-tRNA synthetases in Arabidopsis thaliana and Phaseolus vulgaris." Duchene A.-M., Peeters N., Dietrich A., Cosset A., Small I.D., Wintz H. J. Biol. Chem. 276:15275-15283(2001) [PubMed: 11278923] [Abstract] Cited for: SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AJ002062 mRNA. Translation: CAA05162.1. AC008030 Genomic DNA. Translation: AAG10608.1. AY050895 mRNA. Translation: AAK92832.1. AY086930 mRNA. Translation: AAM64494.1. Different initiation.
IPI	IPI00528368. IPI00760319.
PIR	D86422.
RefSeq	NP_564337.1.
UniGene	At.73 Rra.24381 Rra.7345 Rsa.7176
3D structure databases
SMR	O23627. Positions 120-721.
ModBase	Search...
Protein-protein interaction databases
STRING	O23627.
Proteomic databases
PRIDE	O23627.
Genome annotation databases
GeneID	839866.
GenomeReviews	Gene locus AT1G29880 in contig CT485782_GR.
KEGG	ath:AT1G29880.
NMPDR	fig|3702.1.peg.3322.
Organism-specific databases
GeneFarm	2677. 262.
TAIR	At1g29880.
Phylogenomic databases
eggNOG	KOG2298.
HOGENOM	HBG319978.
InParanoid	O23627.
OMA	GSITWAD.
PhylomeDB	O23627.
Enzyme and pathway databases
BRENDA	6.1.1.14. 302.
Gene expression databases
ArrayExpress	O23627.
Genevestigator	O23627.
GermOnline	AT1G29880. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR002314. aa-tRNA-synt_IIb_cons-dom. IPR006195. aa-tRNA-synth_II_cons-dom. IPR004154. Anticodon_bd. IPR009068. S15_NS1_RNA_bd. IPR002315. tRNA-synt_gly. IPR018160. tRNA-synth_gly_a2dimer_C. IPR000738. WHEP-TRS. [Graphical view]
Gene3D	G3DSA:3.40.50.800. Anticodon_bd. 1 hit.
PANTHER	PTHR10745. tRNA-synt_gly. 1 hit.
Pfam	PF03129. HGTP_anticodon. 1 hit. PF00587. tRNA-synt_2b. 1 hit. PF00458. WHEP-TRS. 1 hit. [Graphical view]
PRINTS	PR01043. TRNASYNTHGLY.
TIGRFAMs	TIGR00389. glyS_dimeric. 1 hit.
PROSITE	PS50862. AA_TRNA_LIGASE_II. 1 hit. PS00762. WHEP_TRS_1. 1 hit. PS51185. WHEP_TRS_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

SYGM1_ARATH

Accession

Primary (citable) accession number: O23627
Secondary accession number(s): Q8LBY0, Q949T7

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	January 1, 1998
Last modified:	February 9, 2010
This is version 79 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)