Q0WL81 · RNL_ARATH

Function

function

Essential component of stress-response pathways entailing repair of RNA breaks with 2',3'-cyclic phosphate and 5'-OH ends (PubMed:23515942).
Tri-functional enzyme that repairs RNA breaks with 2',3'-cyclic-PO4 and 5'-OH ends. The ligation activity requires three sequential enzymatic activities: opening of the 2'3'-cyclic phosphodiester bond of the 5' half-tRNA leaving a 2'-phosphomonoester (CPDase activity), phosphorylation of the 5' terminus of the 3' half-tRNA in the presence of ATP (kinase activity) and ligation of the two tRNA halves in an ATP-dependent reaction (ligase activity) (PubMed:23515942, PubMed:24554441).
Deficient in transferring AMP to pRNA(OH) to form AppRNA(OH) but proficient at sealing pre-adenylylated AppRNA(OH) (PubMed:23515942).
CPDase and kinase reactions are almost insensitive to RNA length, whereas the ligase activity decreases with shorter RNA size. Can also splice DNA ended by a single 3'-terminal ribonucleoside 2',3'-cyclic-PO4 (PubMed:24554441).
Binds to mRNA, mature and immature (PubMed:20844078).
Exhibits tRNA ligase activity in vitro (PubMed:15653639, PubMed:24554441).
Required for the splicing of precursor tRNA molecules containing introns (PubMed:16428247, PubMed:20844078).
Can circularize an intron cleaved from a pre-tRNA by splicing endonuclease in vitro (PubMed:20844078).
Seems not involved in unfolded protein response (UPR) in the endoplasmic reticulum (PubMed:20844078).
Involved in auxin signaling and polar transport during organ morphogenesis (PubMed:25892242).

Catalytic activity

  • ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate.
    EC:6.5.1.3 (UniProtKB | ENZYME | Rhea)

Cofactor

Mg2+ (UniProtKB | Rhea| CHEBI:18420 )

Note: Requires the presence of Mg2+ to exhibit tRNA ligase activity.

Activity regulation

Requires the presence of NTP, preferentially ATP rather than dATP, UTP, CTP and GTP, respectively, to mediate ribonucleotide 5'-phosphorylation.

Features

Showing features for active site.

TypeIDPosition(s)Description
Active site152N6-AMP-lysine intermediate

GO annotations

AspectTerm
Cellular Componentcytoplasm
Cellular Componentnucleus
Molecular FunctionATP binding
Molecular Functionendonuclease activity
Molecular Functionkinase activity
Molecular Functionmetal ion binding
Molecular FunctionmRNA binding
Molecular FunctionRNA ligase (ATP) activity
Biological Processauxin-activated signaling pathway
Biological Processphosphorylation
Biological Processregulation of auxin mediated signaling pathway
Biological ProcessRNA repair
Biological Processtranslation
Biological ProcesstRNA splicing, via endonucleolytic cleavage and ligation

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    tRNA ligase 1
  • EC number
  • Short names
    AtRLG1
    ; AtRNL
    ; AtRlg1p
  • Alternative names
    • Protein AT.I.24-9

Gene names

    • Name
      RNL
    • Synonyms
      RLG1
    • ORF names
      T6D22.1
    • Ordered locus names
      At1g07910

Organism names

  • Taxonomic identifier
  • Strain
    • cv. Columbia
  • Taxonomic lineage
    Eukaryota > Viridiplantae > Streptophyta > Embryophyta > Tracheophyta > Spermatophyta > Magnoliopsida > eudicotyledons > Gunneridae > Pentapetalae > rosids > malvids > Brassicales > Brassicaceae > Camelineae > Arabidopsis

Accessions

  • Primary accession
    Q0WL81
  • Secondary accessions
    • Q0WVN4
    • Q0WWW5
    • Q96312
    • Q9LN14

Proteomes

Organism-specific databases

Genome annotation databases

Subcellular Location

Nucleus
Cytoplasm
Note: Associated on polysomes.

Keywords

Phenotypes & Variants

Disruption phenotype

Abnormal auxin responses leading to altered root physiology (e.g. elongation, meristem morphology and gravitropism) and aberrations in cotyledon number and venation. At later developmental stages, reduced apical dominance and aberrations in lateral organ positioning at inflorescence stems.

Features

Showing features for mutagenesis.

TypeIDPosition(s)Description
Mutagenesis152Loss of tRNA ligase activity due to impaired ligase activity, but normal end-healing.
Mutagenesis218Loss of tRNA ligase activity.
Mutagenesis326Loss of tRNA ligase activity.
Mutagenesis541Loss of tRNA ligase activity.
Mutagenesis543Loss of tRNA ligase activity.
Mutagenesis700-701Loss of kinase activity, but conserved CPDase activity.
Mutagenesis701Loss of tRNA ligase activity.
Mutagenesis726Loss of tRNA ligase activity due to impaired kinase activity, but conserved CPDase activity.
Mutagenesis804Reduced tRNA ligase activity.
Mutagenesis999Reduced tRNA ligase activity due to reduced CPDase activity.
Mutagenesis1001Loss of tRNA ligase activity due to impaired CPDase activity, but conserved kinase activity.
Mutagenesis1060Loss of tRNA ligase activity due to reduced CPDase activity.
Mutagenesis1062Reduced CPDase activity.

Variants

We now provide the "Disease & Variants" viewer in its own tab.

The viewer provides 90 variants from UniProt as well as other sources including ClinVar and dbSNP.

Go to variant viewer

PTM/Processing

Features

Showing features for chain.

TypeIDPosition(s)Description
ChainPRO_00004393421-1104tRNA ligase 1

Proteomic databases

PTM databases

Expression

Tissue specificity

Mainly expressed in proliferating cells and tissues such as root meristems, the vasculature of developing plantlets, flowers and elongating tissue.

Developmental stage

During lateral root formation, already visible in stage I lateral root primordia, and accumulates at strong levels during later stages of root development.

Gene expression databases

Interaction

Protein-protein interaction databases

Family & Domains

Domain

Has three domains each corresponding to an enzymatic activity, namely in N- to C-terminal order: ligase, kinase and cyclic phosphodiesterase (CPDase).

Sequence similarities

Belongs to the TRL1 family.

Phylogenomic databases

Family and domain databases

Sequence & Isoform

Align isoforms (2)
  • Sequence status
    Complete

This entry describes 2 isoforms produced by Alternative splicing. Additional isoforms seem to exist.

Q0WL81-1

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.

  • Length
    1,104
  • Mass (Da)
    123,205
  • Last updated
    2006-09-05 v1
  • MD5 Checksum
    5C385E704DEC2DB06EE5723FAB4C53E7
MDAPFESGDSSATVVAEAVNNQFGGLSLKESNTNAPVLPSQTTSNHRVQNLVWKPKSYGTVSGSSSATEVGKTSAVSQIGSSGDTKVGLNLSKIFGGNLLEKFSVDKSTYCHAQIRATFYPKFENEKTDQEIRTRMIEMVSKGLATLEVSLKHSGSLFMYAGHKGGAYAKNSFGNIYTAVGVFVLSRMFREAWGTKAPKKEAEFNDFLEKNRMCISMELVTAVLGDHGQRPLDDYVVVTAVTELGNGKPQFYSTSEIISFCRKWRLPTNHVWLFSTRKSVTSFFAAFDALCEEGIATSVCRALDEVADISVPASKDHVKVQGEILEGLVARIVSSQSSRDMENVLRDHPPPPCDGANLDLGLSLREICAAHRSNEKQQMRALLRSVGPSFCPSDVEWFGDESHPKSADKSVITKFLQSQPADYSTSKLQEMVRLMKEKRLPAAFKCYHNFHRAEDISPDNLFYKLVVHVHSDSGFRRYHKEMRHMPSLWPLYRGFFVDINLFKSNKGRDLMALKSIDNASENDGRGEKDGLADDDANLMIKMKFLTYKLRTFLIRNGLSILFKDGAAAYKTYYLRQMKIWGTSDGKQKELCKMLDEWAAYIRRKCGNDQLSSSTYLSEAEPFLEQYAKRSPKNHILIGSAGNLVRTEDFLAIVDGDLDEEGDLVKKQGVTPATPEPAVKEAVQKDEGLIVFFPGIPGSAKSALCKELLNAPGGFGDDRPVHTLMGDLVKGKYWPKVADERRKKPQSIMLADKNAPNEDVWRQIEDMCRRTRASAVPIVADSEGTDTNPYSLDALAVFMFRVLQRVNHPGKLDKESSNAGYVLLMFYHLYEGKNRNEFESELIERFGSLIKMPLLKSDRTPLPDPVKSVLEEGIDLFNLHSRRHGRLESTKGTYAAEWTKWEKQLRDTLVANSEYLSSIQVPFESMVHQVREELKTIAKGDYKPPSSEKRKHGSIVFAAINLPATQVHSLLEKLAAANPTMRSFLEGKKKSIQEKLERSHVTLAHKRSHGVATVASYSQHLNREVPVELTELIYNDKMAALTAHVGSVDGETVVSKNEWPHVTLWTAEGVTAKEANTLPQLYLEGKASRLVIDPPVSISGPLEFF

Q0WL81-2

  • Name
    2
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical

Computationally mapped potential isoform sequences

There is 1 potential isoform mapped to this entry

View all
EntryEntry nameGene nameLength
A0A2H1ZEA2A0A2H1ZEA2_ARATHRNL1177

Sequence caution

The sequence AAF79821.1 differs from that shown. Reason: Erroneous gene model prediction

Features

Showing features for alternative sequence, sequence conflict.

Type
IDPosition(s)Description
Alternative sequenceVSP_0588281-576in isoform 2
Sequence conflict945in Ref. 4; AAB07881
Sequence conflict1088in Ref. 3; BAE98814

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
AC026875
EMBL· GenBank· DDBJ
AAF79821.1
EMBL· GenBank· DDBJ
Genomic DNA Sequence problems.
CP002684
EMBL· GenBank· DDBJ
AEE28210.1
EMBL· GenBank· DDBJ
Genomic DNA
AK226218
EMBL· GenBank· DDBJ
BAE98383.1
EMBL· GenBank· DDBJ
mRNA
AK226707
EMBL· GenBank· DDBJ
BAE98814.1
EMBL· GenBank· DDBJ
mRNA
AK230326
EMBL· GenBank· DDBJ
BAF02126.1
EMBL· GenBank· DDBJ
mRNA
U63815
EMBL· GenBank· DDBJ
AAB07881.1
EMBL· GenBank· DDBJ
Genomic DNA

Genome annotation databases

Similar Proteins

Disclaimer

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