P00971 · RLIG_BPT4
- ProteinRNA ligase 1
- Gene63
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids374 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Involved in countering a host defense mechanism which, following viral infection, activates the host anticodon nuclease and shuts off viral translation. Repairs 5'-PO4 and 3'-OH groups in the cleaved host tRNA (PubMed:16671895, PubMed:17068206, PubMed:2444436).
The nick ligation reaction entails three nucleotidyl transfer steps (PubMed:12766156).
In the first step, the RNA ligase reacts with ATP in the absence of nucleic acid to form a covalent ligase-AMP intermediate and release pyrophosphate (PubMed:12766156).
In step 2, the ligase-AMP binds to the nicked duplex nucleic acid and transfers the adenylate to the 5'-PO4 terminus to form an adenylylated nicked intermediate (PubMed:12766156).
In step 3, the RNA ligase directs the attack of the nick 3'-OH on the 5'-phosphoanhydride linkage, resulting in a repaired 3'-5' phosphodiester and release of AMP (By similarity) (PubMed:12766156).
The nick ligation reaction entails three nucleotidyl transfer steps (PubMed:12766156).
In the first step, the RNA ligase reacts with ATP in the absence of nucleic acid to form a covalent ligase-AMP intermediate and release pyrophosphate (PubMed:12766156).
In step 2, the ligase-AMP binds to the nicked duplex nucleic acid and transfers the adenylate to the 5'-PO4 terminus to form an adenylylated nicked intermediate (PubMed:12766156).
In step 3, the RNA ligase directs the attack of the nick 3'-OH on the 5'-phosphoanhydride linkage, resulting in a repaired 3'-5' phosphodiester and release of AMP (By similarity) (PubMed:12766156).
Catalytic activity
Cofactor
Note: Binds 2 magnesium ions that perform the catalytic activity via a two-metal mechanism (PubMed:16263720, PubMed:28223499).
One of the catalytic Mg2+, which is coordinated by 5 water molecules, engages the lysine nucleophile and the ATP alpha phosphate while the Mg2+ orients the PPi leaving group (PubMed:28223499).
One of the catalytic Mg2+, which is coordinated by 5 water molecules, engages the lysine nucleophile and the ATP alpha phosphate while the Mg2+ orients the PPi leaving group (PubMed:28223499).
pH Dependence
Optimum pH is 8.0.
Features
Showing features for binding site, active site, site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 37 | ATP (UniProtKB | ChEBI) | ||||
Sequence: Y | ||||||
Binding site | 54 | ATP (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Binding site | 75 | ATP (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Active site | 99 | N6-AMP-lysine intermediate | ||||
Sequence: K | ||||||
Binding site | 159 | ATP (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Site | 159 | Essential for RNA ligase activity | ||||
Sequence: E | ||||||
Binding site | 240 | ATP (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 242 | ATP (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Site | 246 | Essential for RNA ligase activity | ||||
Sequence: Y | ||||||
Binding site | 272 | Mg2+ (UniProtKB | ChEBI); catalytic | ||||
Sequence: D |
GO annotations
Aspect | Term | |
---|---|---|
Molecular Function | ATP binding | |
Molecular Function | metal ion binding | |
Molecular Function | RNA ligase (ATP) activity | |
Biological Process | RNA repair | |
Biological Process | virus tail fiber assembly |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameRNA ligase 1
- EC number
- Alternative names
Gene names
Organism names
- Taxonomic lineageViruses > Duplodnaviria > Heunggongvirae > Uroviricota > Caudoviricetes > Straboviridae > Tevenvirinae > Tequatrovirus
- Virus hosts
Accessions
- Primary accessionP00971
Proteomes
Phenotypes & Variants
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 37 | No effect on the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and on tRNA repair. | ||||
Sequence: Y → A | ||||||
Mutagenesis | 45 | Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and on tRNA repair. | ||||
Sequence: W → A | ||||||
Mutagenesis | 54 | 65% loss of adenylyltransferase activity. 70% loss of ligase activity. | ||||
Sequence: R → A | ||||||
Mutagenesis | 75 | 95% loss of adenylyltransferase activity. Impaired ligase activity. | ||||
Sequence: K → A | ||||||
Mutagenesis | 77 | 90% loss of adenylyltransferase activity. Impaired ligase activity. | ||||
Sequence: F → A | ||||||
Mutagenesis | 99 | Complete loss of adenylyltransferase activity and ligase activity. | ||||
Sequence: K → A | ||||||
Mutagenesis | 99 | Complete loss of ligase activity. | ||||
Sequence: K → N | ||||||
Mutagenesis | 99 | About 50% loss of ligase activity. | ||||
Sequence: K → R | ||||||
Mutagenesis | 100 | No effect on ligase activity. | ||||
Sequence: E → Q | ||||||
Mutagenesis | 100 | About 50% loss of ligase activity. | ||||
Sequence: E → T | ||||||
Mutagenesis | 101 | Complete loss of ligase activity. | ||||
Sequence: D → N, S, or E | ||||||
Mutagenesis | 102 | Complete loss of adenylyltransferase activity and ligase activity. | ||||
Sequence: G → A | ||||||
Mutagenesis | 119 | Increased adenylyltransferase activity. No effect on ligase activity. | ||||
Sequence: K → A | ||||||
Mutagenesis | 159 | Complete loss of ligation of 5'-PO4 and 3'-OH termini of the RNA strand and complete loss of tRNA repair. | ||||
Sequence: E → A | ||||||
Mutagenesis | 165 | Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand; no effect on tRNA repair. | ||||
Sequence: N → A | ||||||
Mutagenesis | 179 | Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand; no effect on tRNA repair. | ||||
Sequence: L → A | ||||||
Mutagenesis | 182 | Complete loss of ligation. | ||||
Sequence: R → A | ||||||
Mutagenesis | 227 | Complete loss of adenylyltransferase activity and ligase activity. | ||||
Sequence: E → A | ||||||
Mutagenesis | 228 | Complete loss of adenylyltransferase activity and ligase activity. | ||||
Sequence: G → A | ||||||
Mutagenesis | 230 | Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand; no effect on tRNA repair. | ||||
Sequence: V → A | ||||||
Mutagenesis | 240 | Complete loss of adenylyltransferase activity and ligase activity. | ||||
Sequence: K → A | ||||||
Mutagenesis | 242 | Complete loss of adenylyltransferase activity and ligase activity. | ||||
Sequence: K → A | ||||||
Mutagenesis | 246 | Complete loss of ligation of 5'-PO4 and 3'-OH termini of the RNA strand and complete loss of tRNA repair; no effect on adenylyltransferase activity. | ||||
Sequence: Y → A | ||||||
Mutagenesis | 272 | No effect on the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and no effect on tRNA repair. | ||||
Sequence: D → A | ||||||
Mutagenesis | 273 | No effect on the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and no effect on tRNA repair. | ||||
Sequence: D → A |
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000164976 | 1-374 | RNA ligase 1 | |||
Sequence: MQELFNNLMELCKDSQRKFFYSDDVSASGRTYRIFSYNYASYSDWLLPDALECRGIMFEMDGEKPVRIASRPMEKFFNLNENPFTMNIDLNDVDYILTKEDGSLVSTYLDGDEILFKSKGSIKSEQALMANGILMNINHHRLRDRLKELAEDGFTANFEFVAPTNRIVLAYQEMKIILLNVRENETGEYISYDDIYKDATLRPYLVERYEIDSPKWIEEAKNAENIEGYVAVMKDGSHFKIKSDWYVSLHSTKSSLDNPEKLFKTIIDGASDDLKAMYADDEYSYRKIEAFETTYLKYLDRALFLVLDCHNKHCGKDRKTYAMEAQGVAKGAGMDHLFGIIMSLYQGYDSQEKVMCEIEQNFLKNYKKFIPEGY |
Structure
Family & Domains
Domain
The N-terminus contains the nucleotidyltransferase domain (PubMed:17585047).
The C-terminus probably confers tRNA specificity (PubMed:17585047).
The C-terminus probably confers tRNA specificity (PubMed:17585047).
Sequence similarities
Belongs to the Tequatrovirus RNA ligase 1 family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length374
- Mass (Da)43,509
- Last updated1986-07-21 v1
- Checksum04388DBA72A8121C
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
X00365 EMBL· GenBank· DDBJ | CAA25107.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
X04140 EMBL· GenBank· DDBJ | CAA27760.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AF158101 EMBL· GenBank· DDBJ | AAD42514.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
M10160 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. |