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O23627 (SYGM1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 94. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | 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
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
Gene names
Name:GLYRS-1
Ordered Locus Names:At1g29880
ORF Names:F1N18.8
OrganismArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length729 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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.6.

Sequence similarities

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

Contains 1 WHEP-TRS domain.

Sequence caution

The sequence AAM64494.1 differs from that shown. Reason: Erroneous initiation.

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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 2828Mitochondrion Potential
Chain29 – 729701Glycine--tRNA ligase 1, mitochondrial
PRO_0000035802

Regions

Domain50 – 10657WHEP-TRS
Nucleotide binding328 – 3303ATP By similarity
Nucleotide binding338 – 3436ATP By similarity
Nucleotide binding454 – 4552ATP By similarity
Nucleotide binding579 – 5824ATP By similarity
Region343 – 3475Substrate binding By similarity
Region575 – 5795Substrate binding By similarity

Sites

Binding site2091Substrate By similarity
Binding site2961Substrate By similarity
Binding site4321Substrate By similarity
Binding site4321Substrate; via carbonyl oxygen By similarity

Natural variations

Alternative sequence1 – 3939Missing in isoform Cytoplasmic.
VSP_018906

Experimental info

Sequence conflict11M → T Ref.5
Sequence conflict821I → M in AAK92832. Ref.4
Sequence conflict6321V → A in AAM64494. Ref.5

Sequences

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

Last modified January 1, 1998. Version 1.
Checksum: BFF40B27571794E6

FASTA72981,944
        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

« Hide

Isoform Cytoplasmic [UniParc].

Checksum: 705B4179AF455F3E
Show »

FASTA69077,231

References

« Hide '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. expand/collapse author list , 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]The Arabidopsis Information Resource (TAIR)
Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: cv. Columbia.
[4]"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. expand/collapse author list , 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.
[5]"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].
[6]"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.
CP002684 Genomic DNA. Translation: AEE31145.1.
AY050895 mRNA. Translation: AAK92832.1.
AY086930 mRNA. Translation: AAM64494.1. Different initiation.
IPIIPI00528368.
IPI00760319.
PIRD86422.
RefSeqNP_564337.1. NM_102728.2.
UniGeneAt.73.

3D structure databases

ProteinModelPortalO23627.
SMRO23627. Positions 52-96, 117-723.
ModBaseSearch...

Protein-protein interaction databases

STRINGO23627.

Proteomic databases

PRIDEO23627.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT1G29880.1; AT1G29880.1; AT1G29880.
GeneID839866.
GenomeReviewsGene locus AT1G29880 in contig CT485782_GR.
KEGGath:AT1G29880.
NMPDRfig|3702.1.peg.3322.

Organism-specific databases

GeneFarm2677. 262.
TAIRAt1g29880.

Phylogenomic databases

eggNOGKOG2298.
HOGENOMHBG319978.
InParanoidO23627.
OMAGSITWAD.
PhylomeDBO23627.
ProtClustDBPLN02734.

Enzyme and pathway databases

BRENDA6.1.1.14. 399.

Gene expression databases

ArrayExpressO23627.
GenevestigatorO23627.
GermOnlineAT1G29880. Arabidopsis thaliana.

Family and domain databases

InterProIPR002314. aa-tRNA-synt_IIb_cons-dom.
IPR006195. aa-tRNA-synth_II.
IPR004154. Anticodon-bd.
IPR009068. S15_NS1_RNA-bd.
IPR002315. tRNA-synt_gly.
IPR000738. WHEP-TRS.
[Graphical view]
Gene3DG3DSA:3.40.50.800. Anticodon_bd. 1 hit.
G3DSA:1.10.287.10. S15_NS1_RNA_bd. 1 hit.
KOK01880.
PANTHERPTHR10745. tRNA-synt_gly. 1 hit.
PfamPF03129. HGTP_anticodon. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
PF00458. WHEP-TRS. 1 hit.
[Graphical view]
PRINTSPR01043. TRNASYNTHGLY.
SMARTSM00991. WHEP-TRS. 1 hit.
[Graphical view]
SUPFAMSSF52954. Anticodon_bd. 1 hit.
SSF47060. S15/NS1_bind. 1 hit.
TIGRFAMsTIGR00389. GlyS_dimeric. 1 hit.
PROSITEPS50862. AA_TRNA_LIGASE_II. 1 hit.
PS00762. WHEP_TRS_1. 1 hit.
PS51185. WHEP_TRS_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameSYGM1_ARATH
AccessionPrimary (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: January 25, 2012
This is version 94 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents