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Annotation rule MF_04149 |
General rule information
[?]
Accession |
MF_04149 |
Dates |
28-FEB-2020 (Created) 7-APR-2020 (Last updated, Version 4) |
Propagated annotation
[?]
Identifier, protein and gene names
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case <FTGroup:1>
Protein name |
RecName:
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Full=RNA ligase 1;
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EC 6.5.1.3;
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AltName:
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Full=Rnl1;
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else
end case
case <OS:Enterobacteria phage T4>
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(Lys). The nick ligation reaction entails three nucleotidyl transfer steps. 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. 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. 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. |
Domain |
The N-terminus contains the nucleotidyltransferase domain. The C-terminus probably confers the tRNA specificity. |
else
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. The nick ligation reaction entails three nucleotidyl transfer steps. 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. 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. 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. |
end case
case <FTGroup:1>
Catalytic activity |
Reaction=ATP + (ribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(ribonucleotide)(m) = (ribonucleotide)(n+m) + AMP + diphosphate.; EC=6.5.1.3; |
Cofactor |
Mg(2+) Note: Binds 2 magnesium ions that perform the catalytic activity via a two-metal mechanism. One of the catalytic Mg(2+), which is coordinated by 5 water molecules, engages the lysine nucleophile and the ATP alpha phosphate while the Mg(2+) orients the PPi leaving group; |
end case
Similarity |
Belongs to the Tequatrovirus RNA ligase 1 family. |
case <FTGroup:1>
end case
From: RLIG_BPT4 (P00971) |
Key
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From
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To
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Description
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Tag
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Condition
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FTGroup
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ACT_SITE
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99
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99
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N6-AMP-lysine intermediate
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K
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1
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METAL
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272
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272
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Magnesium; catalytic
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D
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1
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BINDING
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37
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37
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ATP
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Y
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BINDING
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54
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|
54
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|
ATP
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|
|
|
R
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BINDING
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75
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|
75
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ATP
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|
|
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K
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|
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BINDING
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159
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|
159
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ATP
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E
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BINDING
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240
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240
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ATP
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|
|
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K
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|
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BINDING
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242
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242
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ATP
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K
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SITE
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159
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159
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Essential for RNA ligase activity
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E
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1
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SITE
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246
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246
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Essential for RNA ligase activity
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Y
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1
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Additional information
[?]
Size range |
300-400 amino acids |
Related rules |
None |
Fusion |
None |