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Literature summary for 6.5.1.3 extracted from

  • Gu, H.; Yoshinari, S.; Ghosh, R.; Ignatochkina, A.V.; Gollnick, P.D.; Murakami, K.S.; Ho, C.K.
    Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis (2016), Nucleic Acids Res., 44, 2337-2347 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 6.5.1.3

Crystallization (Commentary)

Crystallization (Comment) Organism
in complex with ATP or AMP, hanging drop vapor diffusion method, using 0.1 MTris-HCl (pH 8.5), 0.2 M lithium sulfate and 40% (w/v) PEG400 Methanothermobacter thermautotrophicus

Protein Variants

Protein Variants Comment Organism
E151A inactive Methanothermobacter thermautotrophicus
E231A inactive Methanothermobacter thermautotrophicus
E256A the mutation shows a moderate effects on step 1 adenylylation (5-20fold decrease in affinity for ATP) as compared to the wild type enzyme Methanothermobacter thermautotrophicus
E95A the mutation shows a moderate effects on step 1 adenylylation (5-20fold decrease in affinity for ATP) as compared to the wild type enzyme Methanothermobacter thermautotrophicus
E96A the mutation shows a moderate effects on step 1 adenylylation (5-20fold decrease in affinity for ATP) as compared to the wild type enzyme Methanothermobacter thermautotrophicus
F175A the mutant forms traced amounts of ligase-AMP intermediates, with more than 40fold decrease in affinity for ATP Methanothermobacter thermautotrophicus
K246A inactive Methanothermobacter thermautotrophicus
K73A the mutant has ATP affinity comparable to the wild type enzyme Methanothermobacter thermautotrophicus
K97A inactive Methanothermobacter thermautotrophicus
N102A inactive Methanothermobacter thermautotrophicus
N99A the mutation shows a moderate effects on step 1 adenylylation (5-20fold decrease in affinity for ATP) as compared to the wild type enzyme Methanothermobacter thermautotrophicus
R104A the mutant forms traced amounts of ligase-AMP intermediates, with more than 40fold decrease in affinity for ATP Methanothermobacter thermautotrophicus
R118A the mutant forms traced amounts of ligase-AMP intermediates, with more than 40fold decrease in affinity for ATP Methanothermobacter thermautotrophicus
R275A the mutation shows a moderate effects on step 1 adenylylation (5-20fold decrease in affinity for ATP) as compared to the wild type enzyme Methanothermobacter thermautotrophicus
R278A the mutation shows a moderate effects on step 1 adenylylation (5-20fold decrease in affinity for ATP) as compared to the wild type enzyme Methanothermobacter thermautotrophicus
R76A the mutation does not have a major effect on all three steps in the ligation reaction Methanothermobacter thermautotrophicus
T117A the mutant has ATP affinity comparable to the wild type enzyme. The mutation favors the reverse RNA adenylylation reaction to deadenylate the 5'-AMP from the RNA-adenylate, thereby inhibiting phosphodiester bond synthesis Methanothermobacter thermautotrophicus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m Methanothermobacter thermautotrophicus
-
 (ribonucleotide)n+m + AMP + diphosphate
-
 ?
ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m Methanothermobacter thermautotrophicus ATCC 29096
-
 (ribonucleotide)n+m + AMP + diphosphate
-
 ?
ATP + [RNA ligase]-L-lysine Methanothermobacter thermautotrophicus
-
 [RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate
-
 ?
ATP + [RNA ligase]-L-lysine Methanothermobacter thermautotrophicus ATCC 29096
-
 [RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate
-
 ?

Organism

Organism UniProt Comment Textmining
Methanothermobacter thermautotrophicus O27289
-
-
Methanothermobacter thermautotrophicus ATCC 29096 O27289
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m
-
 Methanothermobacter thermautotrophicus (ribonucleotide)n+m + AMP + diphosphate
-
 ?
ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m
-
 Methanothermobacter thermautotrophicus ATCC 29096 (ribonucleotide)n+m + AMP + diphosphate
-
 ?
ATP + [RNA ligase]-L-lysine
-
 Methanothermobacter thermautotrophicus [RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate
-
 ?
ATP + [RNA ligase]-L-lysine
-
 Methanothermobacter thermautotrophicus ATCC 29096 [RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate
-
 ?

Subunits

Subunits Comment Organism
? 2 * 42000, SDS-PAGE Methanothermobacter thermautotrophicus

Synonyms

Synonyms Comment Organism
ATP-dependent RNA ligase
-
 Methanothermobacter thermautotrophicus
RNL
-
 Methanothermobacter thermautotrophicus