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6.5.1.3: RNA ligase (ATP)

This is an abbreviated version!
For detailed information about RNA ligase (ATP), go to the full flat file.

Word Map on EC 6.5.1.3

Reaction

(ribonucleotide)n-3'-hydroxyl
+
5'-(5'-diphosphoadenosine)-(ribonucleotide)m
=
(ribonucleotide)n+m
 +
AMP

Synonyms

ATP-dependent RNA ligase, b1-10t, bacteriophage RNA ligase, band IV protein, class I ligase, class I RNA ligase ribozyme, DraRnI, DraRnl, DREL, gp24.1, P52, phage Rnl2, Polynucleotide synthetase, Polyribonucleotide ligase, Polyribonucleotide synthase (ATP), REL1, Ribonucleic ligase, ribonucleprotein editing complex, RM378 RNA ligase, RNA editing ligase 1, RNA ligase, RNA ligase (ATP), RNA ligase 1, RNA ligase 2, RNA ligase ribozyme, RNA-editing ligase 1, RNL, Rnl1, Rnl2, Rnl5, RnlA, RtcA, rtcB, Synthetase, polyribonucleotide, T4 RNA ligase, T4 RNA ligase 1, T4 RNA ligase 2, T4Rnl2, TbMP52, TbREL1, thermostable RNA ligase 1, Trl1

ECTree

     6 Ligases
         6.5 Forming phosphoric-ester bonds
             6.5.1 Ligases that form phosphoric-ester bonds (only sub-subclass identified to date)
                6.5.1.3 RNA ligase (ATP)

Crystallization

Crystallization on EC 6.5.1.3 - RNA ligase (ATP)

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
2.6 A crystal structure
-
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
hanging drop vapor diffusion method, using 0.1 M HEPES pH 6.5, 30% (w/v) PEG6000
-
2.2 A resolution, crystal structure of a complete RNA ligase, Rnl1, in complex with adenosine 5'-(alpha,beta-methylenetriphosphate)
Tequatrovirus T4
-
crystal structure of the ligase domain with AMP bound at the active site, space group P2(1)2(1)2, a = 57.72 A, b = 89.89 A, c = 47.74 A
Tequatrovirus T4
hanging-drop vapor diffusion. Crystal structures of: 1. Covalent Rnl2-AMP intermediate, 2. Rnl2 bound to an adenylylated nicked duplex, captured immediately following reaction step 2, 3. Rnl2 at an adenylylated nick in a state poised for step 3. These structures illuminate the stereochemistry of nucleotidyl transfer and reveal how remodeling of active-site contacts and conformational changes propel the ligation reaction forward
Tequatrovirus T4
crystal structure of the catalytic domain of TbREL1 at 1.2 A resolution, in complex with ATP and magnesium.The magnesium ion interacts with the beta and gamma-phosphate groups and is almost perfectly octahedrally coordinated by six phosphate and water oxygen atoms. Sitting-drop, vapor-diffusion with 100 mM HEPES, 100 mM Mg2+ and 35% (w/v) PEG3350 at pH 7.0. The crystal belongs to space group P2(1), with cell dimensions of a = 44.9 A, b = 58.6 A, c = 53.0 A and beta = 100.2°, and one molecule in the asymmetric unit
-
virtual screen of REL1 crystal structure for inhibitors