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Literature summary 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

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
6.5.1.3 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

EC Number Protein Variants Comment Organism
6.5.1.3 E151A inactive Methanothermobacter thermautotrophicus
6.5.1.3 E231A inactive Methanothermobacter thermautotrophicus
6.5.1.3 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
6.5.1.3 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
6.5.1.3 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
6.5.1.3 F175A the mutant forms traced amounts of ligase-AMP intermediates, with more than 40fold decrease in affinity for ATP Methanothermobacter thermautotrophicus
6.5.1.3 K246A inactive Methanothermobacter thermautotrophicus
6.5.1.3 K73A the mutant has ATP affinity comparable to the wild type enzyme Methanothermobacter thermautotrophicus
6.5.1.3 K97A inactive Methanothermobacter thermautotrophicus
6.5.1.3 N102A inactive Methanothermobacter thermautotrophicus
6.5.1.3 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
6.5.1.3 R104A the mutant forms traced amounts of ligase-AMP intermediates, with more than 40fold decrease in affinity for ATP Methanothermobacter thermautotrophicus
6.5.1.3 R118A the mutant forms traced amounts of ligase-AMP intermediates, with more than 40fold decrease in affinity for ATP Methanothermobacter thermautotrophicus
6.5.1.3 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
6.5.1.3 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
6.5.1.3 R76A the mutation does not have a major effect on all three steps in the ligation reaction Methanothermobacter thermautotrophicus
6.5.1.3 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)

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

Organism

EC Number Organism UniProt Comment Textmining
6.5.1.3 Methanothermobacter thermautotrophicus O27289
-
-
6.5.1.3 Methanothermobacter thermautotrophicus ATCC 29096 O27289
-
-

Substrates and Products (Substrate)

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

Subunits

EC Number Subunits Comment Organism
6.5.1.3 ? 2 * 42000, SDS-PAGE Methanothermobacter thermautotrophicus

Synonyms

EC Number Synonyms Comment Organism
6.5.1.3 ATP-dependent RNA ligase
-
 Methanothermobacter thermautotrophicus
6.5.1.3 RNL
-
 Methanothermobacter thermautotrophicus