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Protein

Serine--tRNA ligase, cytoplasmic

Gene

At5g27470

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).By similarity

Catalytic activityi

ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser).
ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec).

Pathwayi: selenocysteinyl-tRNA(Sec) biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes L-seryl-tRNA(Sec) from L-serine and tRNA(Sec).
Proteins known to be involved in this subpathway in this organism are:
  1. Serine--tRNA ligase, chloroplastic/mitochondrial (OVA7), Serine--tRNA ligase, cytoplasmic (At5g27470)
This subpathway is part of the pathway selenocysteinyl-tRNA(Sec) biosynthesis, which is itself part of Aminoacyl-tRNA biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-seryl-tRNA(Sec) from L-serine and tRNA(Sec), the pathway selenocysteinyl-tRNA(Sec) biosynthesis and in Aminoacyl-tRNA biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei285 – 2851ATP; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei292 – 2921SerineBy similarity
Binding sitei396 – 3961SerineBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi269 – 2713ATPBy similarity
Nucleotide bindingi358 – 3614ATPBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Aminoacyl-tRNA synthetase, Ligase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciARA:AT5G27470-MONOMER.
UniPathwayiUPA00906; UER00895.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine--tRNA ligase, cytoplasmicCurated (EC:6.1.1.11Curated)
Alternative name(s):
Seryl-tRNA synthetaseCurated
Short name:
SerRSCurated
Seryl-tRNA(Ser/Sec) synthetaseCurated
Gene namesi
Ordered Locus Names:At5g27470
ORF Names:F21A20_180
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G27470.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 451451Serine--tRNA ligase, cytoplasmicPRO_0000122195Add
BLAST

Proteomic databases

PaxDbiQ39230.
PRIDEiQ39230.

Expressioni

Gene expression databases

GenevisibleiQ39230. AT.

Interactioni

Subunit structurei

Homodimer. The tRNA molecule binds across the dimer (By similarity).By similarity

Protein-protein interaction databases

STRINGi3702.AT5G27470.1.

Structurei

3D structure databases

ProteinModelPortaliQ39230.
SMRiQ39230. Positions 1-435.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni238 – 2403Serine bindingBy similarity

Domaini

Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding.By similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2509. Eukaryota.
COG0172. LUCA.
HOGENOMiHOG000035937.
InParanoidiQ39230.
KOiK01875.
OMAiVGWSPCF.
PhylomeDBiQ39230.

Family and domain databases

Gene3Di1.10.287.40. 1 hit.
InterProiIPR002314. aa-tRNA-synt_IIb.
IPR006195. aa-tRNA-synth_II.
IPR002317. Ser-tRNA-ligase_type_1.
IPR015866. Ser-tRNA-synth_1_N.
IPR010978. tRNA-bd_arm.
[Graphical view]
PANTHERiPTHR11778. PTHR11778. 1 hit.
PfamiPF02403. Seryl_tRNA_N. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
[Graphical view]
PIRSFiPIRSF001529. Ser-tRNA-synth_IIa. 1 hit.
PRINTSiPR00981. TRNASYNTHSER.
SUPFAMiSSF46589. SSF46589. 1 hit.
TIGRFAMsiTIGR00414. serS. 1 hit.
PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q39230-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLDINLFREE KGNNPEIIRE SQRRRFASVE IVDEIIKLDK EWRQRQFEVD
60 70 80 90 100
SFRKEFNKLN KQVAQLKIKK EDASEIIQQT EKNKQDSTAK EAEVREAYAA
110 120 130 140 150
LKAKLEQVGN LVHDSVPVDK DEANNLVIKL WGEKRFSTPG LKLKNHVDLV
160 170 180 190 200
ELLGIADTKR GAEIAGARGF FLKGDGLMLN QALINFGLTF LKKRGFTGLQ
210 220 230 240 250
PPFFMRKDVM AKCAQLAQFD EELYKVTGEG DDKYLIATAE QPLCAYHIDE
260 270 280 290 300
WIHPTELPLR YAGYSSCFRK EAGSHGRDTL GIFRVHQFEK IEQFCITGPN
310 320 330 340 350
ENASWEMLDE MMKNSEDFYQ ALKLPYQIVS IVSGALNDAA AKKYDLEAWF
360 370 380 390 400
PSSETFRELV SCSNCTDYQA RRLEIRYGQK KSNEQTKQYV HMLNSTLTAT
410 420 430 440 450
ERTICCILEN YQREDGVDIP EVLQPFMGGE TFLPFKAKPV VADTKGKKSK

A
Length:451
Mass (Da):51,629
Last modified:November 1, 1996 - v1
Checksum:iB13D71EF87236AAF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z70313 mRNA. Translation: CAA94388.1.
AC007123 Genomic DNA. No translation available.
CP002688 Genomic DNA. Translation: AED93692.1.
AF360352 mRNA. Translation: AAK28648.1.
AY051054 mRNA. Translation: AAK93731.1.
PIRiS71293.
RefSeqiNP_198099.1. NM_122629.2.
UniGeneiAt.24387.

Genome annotation databases

EnsemblPlantsiAT5G27470.1; AT5G27470.1; AT5G27470.
GeneIDi832806.
GrameneiAT5G27470.1; AT5G27470.1; AT5G27470.
KEGGiath:AT5G27470.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z70313 mRNA. Translation: CAA94388.1.
AC007123 Genomic DNA. No translation available.
CP002688 Genomic DNA. Translation: AED93692.1.
AF360352 mRNA. Translation: AAK28648.1.
AY051054 mRNA. Translation: AAK93731.1.
PIRiS71293.
RefSeqiNP_198099.1. NM_122629.2.
UniGeneiAt.24387.

3D structure databases

ProteinModelPortaliQ39230.
SMRiQ39230. Positions 1-435.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT5G27470.1.

Proteomic databases

PaxDbiQ39230.
PRIDEiQ39230.

Protocols and materials databases

DNASUi832806.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G27470.1; AT5G27470.1; AT5G27470.
GeneIDi832806.
GrameneiAT5G27470.1; AT5G27470.1; AT5G27470.
KEGGiath:AT5G27470.

Organism-specific databases

TAIRiAT5G27470.

Phylogenomic databases

eggNOGiKOG2509. Eukaryota.
COG0172. LUCA.
HOGENOMiHOG000035937.
InParanoidiQ39230.
KOiK01875.
OMAiVGWSPCF.
PhylomeDBiQ39230.

Enzyme and pathway databases

UniPathwayiUPA00906; UER00895.
BioCyciARA:AT5G27470-MONOMER.

Miscellaneous databases

PROiQ39230.

Gene expression databases

GenevisibleiQ39230. AT.

Family and domain databases

Gene3Di1.10.287.40. 1 hit.
InterProiIPR002314. aa-tRNA-synt_IIb.
IPR006195. aa-tRNA-synth_II.
IPR002317. Ser-tRNA-ligase_type_1.
IPR015866. Ser-tRNA-synth_1_N.
IPR010978. tRNA-bd_arm.
[Graphical view]
PANTHERiPTHR11778. PTHR11778. 1 hit.
PfamiPF02403. Seryl_tRNA_N. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
[Graphical view]
PIRSFiPIRSF001529. Ser-tRNA-synth_IIa. 1 hit.
PRINTSiPR00981. TRNASYNTHSER.
SUPFAMiSSF46589. SSF46589. 1 hit.
TIGRFAMsiTIGR00414. serS. 1 hit.
PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A cDNA clone encoding Arabidopsis thaliana seryl-tRNA synthetase."
    Peeters N.M., Small I.D.
    Plant Gene Register PGR96-047
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. Columbia.
  2. "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
    Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.
    , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
    Nature 408:823-826(2000) [PubMed] [Europe PMC] [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.
    , 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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Requirement of aminoacyl-tRNA synthetases for gametogenesis and embryo development in Arabidopsis."
    Berg M., Rogers R., Muralla R., Meinke D.
    Plant J. 44:866-878(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  6. "Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in Arabidopsis thaliana."
    Duchene A.-M., Giritch A., Hoffmann B., Cognat V., Lancelin D., Peeters N.M., Zaepfel M., Marechal-Drouard L., Small I.D.
    Proc. Natl. Acad. Sci. U.S.A. 102:16484-16489(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.

Entry informationi

Entry nameiSYSC_ARATH
AccessioniPrimary (citable) accession number: Q39230
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: February 17, 2016
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  2. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.