Q0WL81 · RNL_ARATH
- ProteintRNA ligase 1
- GeneRNL
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids1104 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
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).
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
Cofactor
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.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Active site | 152 | N6-AMP-lysine intermediate | |||
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytoplasm | |
Cellular Component | nucleus | |
Molecular Function | ATP binding | |
Molecular Function | endonuclease activity | |
Molecular Function | kinase activity | |
Molecular Function | metal ion binding | |
Molecular Function | mRNA binding | |
Molecular Function | RNA ligase (ATP) activity | |
Biological Process | auxin-activated signaling pathway | |
Biological Process | phosphorylation | |
Biological Process | regulation of auxin mediated signaling pathway | |
Biological Process | RNA repair | |
Biological Process | translation | |
Biological Process | tRNA splicing, via endonucleolytic cleavage and ligation |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nametRNA ligase 1
- EC number
- Short namesAtRLG1 ; AtRNL ; AtRlg1p
- Alternative names
Gene names
Organism names
- Strain
- Taxonomic lineageEukaryota > Viridiplantae > Streptophyta > Embryophyta > Tracheophyta > Spermatophyta > Magnoliopsida > eudicotyledons > Gunneridae > Pentapetalae > rosids > malvids > Brassicales > Brassicaceae > Camelineae > Arabidopsis
Accessions
- Primary accessionQ0WL81
- Secondary accessions
Proteomes
Organism-specific databases
Genome annotation databases
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.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Mutagenesis | 152 | Loss of tRNA ligase activity due to impaired ligase activity, but normal end-healing. | |||
Mutagenesis | 218 | Loss of tRNA ligase activity. | |||
Mutagenesis | 326 | Loss of tRNA ligase activity. | |||
Mutagenesis | 541 | Loss of tRNA ligase activity. | |||
Mutagenesis | 543 | Loss of tRNA ligase activity. | |||
Mutagenesis | 700-701 | Loss of kinase activity, but conserved CPDase activity. | |||
Mutagenesis | 701 | Loss of tRNA ligase activity. | |||
Mutagenesis | 726 | Loss of tRNA ligase activity due to impaired kinase activity, but conserved CPDase activity. | |||
Mutagenesis | 804 | Reduced tRNA ligase activity. | |||
Mutagenesis | 999 | Reduced tRNA ligase activity due to reduced CPDase activity. | |||
Mutagenesis | 1001 | Loss of tRNA ligase activity due to impaired CPDase activity, but conserved kinase activity. | |||
Mutagenesis | 1060 | Loss of tRNA ligase activity due to reduced CPDase activity. | |||
Mutagenesis | 1062 | Reduced 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.
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Chain | PRO_0000439342 | 1-1104 | tRNA 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
Structure
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
- Sequence statusComplete
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.
- Name1
- Length1,104
- Mass (Da)123,205
- Last updated2006-09-05 v1
- MD5 Checksum5C385E704DEC2DB06EE5723FAB4C53E7
Q0WL81-2
- Name2
- Differences from canonical
- 1-576: Missing
Computationally mapped potential isoform sequences
There is 1 potential isoform mapped to this entry
Entry | Entry name | Gene name | Length | ||
---|---|---|---|---|---|
A0A2H1ZEA2 | A0A2H1ZEA2_ARATH | RNL | 1177 |
Sequence caution
Features
Showing features for alternative sequence, sequence conflict.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Alternative sequence | VSP_058828 | 1-576 | in isoform 2 | ||
Sequence conflict | 945 | in Ref. 4; AAB07881 | |||
Sequence conflict | 1088 | in Ref. 3; BAE98814 | |||
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
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 |