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.

Reaction

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)

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Results	in table
2	Activating Compound
2439	AA Sequence
7	Application
1	CAS Registry Number
24	Cloned(Commentary)
1	Cofactor
8	Crystallization (Commentary)
44	Disease/ Diagnostics
2	General Information
3	General Stability
4	IC50 Value
43	Inhibitors
7	kcat/KM [mM/s]
18	KM Value [mM]
10	Localization
25	Metals/Ions
14	Molecular Weight [Da]
42	Natural Substrates/ Products (Substrates)
79	Organism
24	PDB ID
15	pH Optimum
6	pH Range
181	Protein Variants
31	Purification (Commentary)
5	Reaction
2	Reaction Type
79	Reference
10	Source Tissue
17	Specific Activity [micromol/min/mg]
7	Storage Stability
136	Substrates and Products (Substrate)
9	Subunits
85	Synonyms
1	Systematic Name
6	Temperature Optimum [°C]
2	Temperature Range [°C]
6	Temperature Stability [°C]
22	Turnover Number [1/s]

Substrates Products

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Substrates Products on EC 6.5.1.3 - RNA ligase (ATP)

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SUBSTRATE

PRODUCT                       

REACTION DIAGRAM

ORGANISM

UNIPROT

COMMENTARY
(Substrate)

LITERATURE
(Substrate)

COMMENTARY
(Product)

LITERATURE
(Product)

Reversibility
r=reversible
ir=irreversible
?=not specified

(deoxyribonucleotide)n

circular (deoxyribonucleotide)n

Methanothermobacter thermautotrophicus

-

-

694452

-

-

?

(ribonucleotide)n

circular (ribonucleotide)n

Methanothermobacter thermautotrophicus

-

-

694452

-

-

?

5'-adenylated cytidine 5',3'-bisphosphate + diguanosine tetraphosphate

Gp4GpCp + pCpGp4GpCp

Tequatrovirus T4

-

-

651061

-

651061

?

8-Bromoadenosine 5'-triphosphate + (ribonucleotide)n + (ribonucleotide)m

8-Bromoadenosine monophosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

2001

-

-

?

8-Sulfoadenosine 5'-triphosphate + (ribonucleotide)n + (ribonucleotide)m

8-Sulfoadenosinemonophosphate + phosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

2001

-

-

?

ATP + (2E,6E)-farnesyl diphosphate

(2E,6E)-farnesyl-triphospho(5')adenosine + diphosphate

Tequatrovirus T4

-

assay contains pyruvate kinase, phosphoenolpyruvate and pyrophosphatase to recover ATP

707449

-

-

ir

ATP + (2E,6E)-farnesyl triphosphate

(2E,6E)-farnesyl-tetraphospho(5')adenosine + diphosphate

Tequatrovirus T4

-

assay contains pyruvate kinase, phosphoenolpyruvate and pyrophosphatase to recover ATP

707449

-

-

ir

ATP + (deoxyribonucleotide)n

adenylyl-(deoxyribonucleotide)n + diphosphate

Methanothermobacter thermautotrophicus

-

-

694452

-

-

?

ATP + (ribonucleotide)n

adenylyl-(ribonucleotide)n + diphosphate

Methanothermobacter thermautotrophicus

-

-

694452

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

?

2 entries

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

68 entries

ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m

(ribonucleotide)n+m + AMP + diphosphate

7 entries

ATP + (RNA)n

?

synthetic construct

-

-

649963

-

-

?

ATP + 5'-aaaCCAGUC

AMP + diphosphate + ?

synthetic construct

-

RNA-DNA hybrid as substrate, chemical step is represented as irreversible, because reverse reaction, pyrophosphorolysis with formation of a triphosphate is 10000000-times slower than the forward reaction

650172

-

650172

ir

ATP + 5'-phosphate termini of RNA

?

Triticum aestivum

-

-

1987

-

-

?

ATP + ATP

P1,P3-bis(5'-adenosyl) triphosphate + ?

Tequatrovirus T4

-

-

651051

-

651051

?

ATP + ATP

P1,P4-bis(5'-adenosyl) tetraphosphate + diphosphate

Tequatrovirus T4

-

-

651051

-

651051

?

ATP + clodronate

adenosine 5'-(beta,gamma-dichloromethylenetriphosphate) + ?

Tequatrovirus T4

-

-

673669

-

-

?

ATP + dimethylallyl diphosphate

dimethylallyl-triphospho(5')adenosine + diphosphate

Tequatrovirus T4

-

assay contains pyruvate kinase, phosphoenolpyruvate and pyrophosphatase to recover ATP

707449

-

-

ir

ATP + etidronate

?

Tequatrovirus T4

-

weak activity

673669

-

-

?

ATP + geranyl diphosphate

geranyl-triphospho(5')adenosine + diphosphate

Tequatrovirus T4

-

assay contains pyruvate kinase, phosphoenolpyruvate and pyrophosphatase to recover ATP

707449

-

-

ir

ATP + geranyl triphosphate

geranyl-tetraphospho(5')adenosine + diphosphate

Tequatrovirus T4

-

assay contains pyruvate kinase, phosphoenolpyruvate and pyrophosphatase to recover ATP

707449

-

-

ir

ATP + isopentenyl diphosphate

adenosine 5'-isopentenyl triphosphate + diphosphate

Tequatrovirus T4

-

assay contains pyruvate kinase, phosphoenolpyruvate and pyrophosphatase to recover ATP

707449

-

-

ir

ATP + isopentenyl triphosphate

isopentenyl-tetraphospho(5')adenosine + diphosphate

Tequatrovirus T4

-

assay contains pyruvate kinase, phosphoenolpyruvate and pyrophosphatase to recover ATP

707449

-

-

ir

ATP + methylenebisphosphonate

adenosine 5'-(beta,gamma-methylenetriphosphate) + ?

Tequatrovirus T4

-

-

673669

-

-

?

ATP + RNA + 5'-aaCCAGUC

AMP + diphosphate + ?

synthetic construct

-

DNA-RNA hybrid

649963

-

649963

?

ATP + [RNA ligase]-L-lysine

[RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate

6 entries

ATPgammaS + ATP

P1,P4-bis(5'-adenosyl) tetraphosphate + thiodiphosphate

Tequatrovirus T4

-

-

651051

-

651051

?

dATP + (ribonucleotide)n + (ribonucleotide)m

dAMP + phosphate + (ribonucleotide)n+m

6 entries

GTP + ATP

P1-(5'-adenosyl),P4-(5'-guanosyl) tetraphosphate + diphosphate

Tequatrovirus T4

-

-

651051

-

651051

?

ITP + (ribonucleotide)n + (ribonucleotide)m

IMP + phosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

2001

-

-

?

additional information

?

-

18 entries

ATP + (ribonucleotide)n + (ribonucleotide)m

?

Leishmania tarentolae

-

possibly involved in posttranscriptional RNA editing process of mitochondrial transcripts

1997

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

?

Leishmania tarentolae UC

-

possibly involved in posttranscriptional RNA editing process of mitochondrial transcripts

1997

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Branchiostoma floridae

C3YGD8

-

716756

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Deinococcus radiodurans

-

DraRnl seals 3'-OH/5'-PO4 RNA nicks in either a duplex RNA or an RNA:DNA hybrid, but it cannot seal 3'-OH/5'-PO4 DNA nicks

662304

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Enterobacteria phage L1

-

the L1 ligase is regioselective for formation of the biologically relevant 5' to 3' phosphodiester bond rather than a 5' to 2' bond

677128

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Escherichia coli

-

T4 RNA ligase 1 can efficiently adenylate DNA oligos with 5' phosphate and 3' blocking group

728488

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Homo sapiens

-

-

1985

-

1985

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Leishmania tarentolae

-

-

1997

-

1997

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Leishmania tarentolae

-

-

663245

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Leishmania tarentolae UC

-

-

1997

-

1997

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Phage TS2126

-

the TS2126 RNA ligase catalyzes both inter- and intra-molecular single-stranded DNA ligation to more than 50% completion in not more than a few hours at an elevated temperature, although favoring intramolecular ligation on RNA and single-stranded DNA substrates

662976

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Rhodothermus phage RM378

-

-

653392

-

653392

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Saccharomyces cerevisiae

-

Trl1 executes the end-healing and end-sealing steps of tRNA splicing, requires a 2'-PO4 end for tRNA splicing in vivo

676215

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

synthetic construct

-

-

650172

-

650172

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

synthetic construct

-

-

653368

-

653368

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

synthetic construct

-

-

653882

-

653882

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

synthetic construct

-

ligates two substrate RNAs, promoting the attack of the 3'-hydroxyl of one substrate upon the 5'-triphosphate of the other substrate with release of diphosphate, reverse of ligation has been detected, but very inefficient, not saturable by soluble amounts of diphosphate

649963

-

649963

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

1910

-

1910

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

1986

-

1986

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

1989

-

1989

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

1990

-

1990

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

1992

-

1992

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

1998

-

1998

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

2000

-

2000

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

2001

-

2001

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

650653

-

650653

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

651051

-

651051

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

651061

-

651061

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

652387

-

652387

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

652429

-

652429

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

653234

-

653234

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

653369

-

653369

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

653679

-

653679

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

654015

-

654015

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

-

652246

-

652246

r

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

P32277

-

653915

-

653915

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

converts linear molecules of polyriboadenylate to circular form by the intramolecular covalent linkage of the 5'-phosphate end to the 3'-hydroxyl terminus

1995

-

1995

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

formation of a phosphodiester bond between a 5'-PO4-terminated oligonucleotide and a 3'-OH terminated oligonucleotide. Intramolecular formation of single-stranded circles with longer oligonucleotides of the type pAp(Ap)nAOH, where n is about 15 or greater. Intermolecular joining of pAp(Ap)3AOH, where the 5'-PO4-terminated oligonucleotide is short enough to prevent apposition of its 3' and 5' ends, to UpUpUOH

1994

-

1994

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

cylization of poly(A)

1993

-

1993

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

the best substrate is [5'-P]polyriboadenylate

1995

-

1995

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

only the di-magnesium-coordinated form Mg2ATP0 reacts with the enzyme, forming the covalent complex E-AMP, the reverse reaction, ATP synthesis, occurs between the mono-magnesium-coordinated diphosphate from MgP2O72- and the enzyme-MgAMP complex

652246

-

652246

r

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

catalyzes the transfer of AMP from the E-AMP complex to diverse compounds, generating the product indicated between parentheses, ATP(Ap4A), NTP (Ap4N), P3 or P4 (p4A or p5A), ADP (Ap3A)

651051

-

651051

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

participates in repair, splicing and editing pathways, reseals broken RNAs or alters their primary structure, catalyzes intramolecular and intermolecular RNA strand joining through ligase-adenylate and RNA adenylate intermediates

653679

-

653679

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

RNA-editing

652387

-

652387

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

neither dATP, GTP, CTP, nor UTP can substitute for ATP. RNA ligation at a 3'-OH/5'-PO4 nick in a double-stranded RNA or an RNA-DNA hybrid

662241

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

Rnl1 has an inherent specificity for sealing tRNA with a break in the anticodon loop. The tRNA specificity is imparted by the C domain

677101

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

the kinetic mechanism of single-turnover nick sealing by T4 Rnl2-AMP is explored by using a rapid mix-quench method and the effects of 3'-OH mispairs and base damage lesions on the rates of nick 5'-adenylylation and phosphodiester synthesis is determined. With respect to the sealing of perfectly paired nicks the rates of step 2 catalysis are rapid (9.5-17.9/sec) and similar in magnitude to the step 3 rates (7.9-32/sec). Rnl2 is kinetically sensitive to all 3'-OH base mispairs

728789

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Triticum aestivum

-

-

1983

-

1983

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Triticum aestivum

-

-

1999

-

1999

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Triticum aestivum

-

-

714026, 714046

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Triticum aestivum

-

poly(A) containing 5'-P-2,3-cyclic P termini

1984

-

1984

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Triticum aestivum

-

RNA substrates containing a 5'-phosphate terminus at one end and either a 2',3'-cyclic phosphate or a 2'-phosphate terminus at the other end. In the latter case the reaction is about 30% as active as with the cyclic derivative

1987

-

1987

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Triticum aestivum

-

participates in an in vitro splicing of yeast transfer RNA precursors containing intervening sequences. Covalently ligates tRNA5' and 3' half-molecules produced by a yeast endonuclease

1988

-

1988

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Triticum aestivum

-

conversion of linear polyribonucleotides into covalently closed circles, formation of a 2'-phosphomonoester,3',5'-phosphodiester linkage

1991

-

1991

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

-

1996

-

1996

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

-

650982

-

650982

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

-

651858

-

651858

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

-

653217

-

653217

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

-

653869

-

653869

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

-

653889

-

653889

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

-

662636, 663245

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

P86927

-

716670

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

RNA editing, essential for proliferation of Trypanosoma brucei

653889

-

653889

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

RNA editing, posttranscriptional insertion and deletion of uridylate residues in mitochondrial transcripts

651858

-

651858

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

RNA editing, posttranscriptional process by which uridine residues are added and deleted from mitochondrial mRNAs

653869

-

653869

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

RNA editing, posttranscriptional RNA processing in which uridylate residues are inserted into and deleted from pre-mRNAs to create start and stop codons, also acts to reseal mRNAs cleaved at incorrect sites

650982

-

650982

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

RNA editing, unique U insertion and U deletion process, involves cycles of pre-mRNA cleavage, terminal U addition or U removal, and religation, band IV is the RNA editing ligase needed to seal in U deletion

653217

-

653217

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Trypanosoma brucei

-

the enzyme is essential for survival of both insect and bloodstream forms of the parasite

662636

-

-

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Vibrio phage KVP40

-

-

654015

-

654015

?

ATP + (ribonucleotide)n + (ribonucleotide)m

AMP + diphosphate + (ribonucleotide)n+m

Vibrio phage KVP40

-

catalyzes RNA end-joining

654015

-

654015

?

ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m

(ribonucleotide)n+m + AMP + diphosphate

Diplonema papillatum

A0A0P0IR96

-

747437

-

-

?

ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m

(ribonucleotide)n+m + AMP + diphosphate

Methanothermobacter thermautotrophicus

-

-

749330

-

-

?

ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m

(ribonucleotide)n+m + AMP + diphosphate

Methanothermobacter thermautotrophicus

O27289

-

748784

-

-

?

ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m

(ribonucleotide)n+m + AMP + diphosphate

Methanothermobacter thermautotrophicus ATCC 29096

O27289

-

748784

-

-

?

ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m

(ribonucleotide)n+m + AMP + diphosphate

Naegleria gruberi

-

-

749172, 749277

-

-

?

ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m

(ribonucleotide)n+m + AMP + diphosphate

Pyrococcus horikoshii

-

-

748777

-

-

?

ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m

(ribonucleotide)n+m + AMP + diphosphate

Tequatrovirus T4

P32277

-

748785

-

-

?

ATP + [RNA ligase]-L-lysine

[RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate

Methanothermobacter thermautotrophicus

-

-

749330

-

-

?

ATP + [RNA ligase]-L-lysine

[RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate

Methanothermobacter thermautotrophicus

O27289

-

748784

-

-

?

ATP + [RNA ligase]-L-lysine

[RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate

Methanothermobacter thermautotrophicus ATCC 29096

O27289

-

748784

-

-

?

ATP + [RNA ligase]-L-lysine

[RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate

Naegleria gruberi

-

-

749172, 749277

-

-

?

ATP + [RNA ligase]-L-lysine

[RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate

Pyrococcus horikoshii

-

-

748777

-

-

?

ATP + [RNA ligase]-L-lysine

[RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate

Tequatrovirus T4

P32277

-

748785

-

-

?

dATP + (ribonucleotide)n + (ribonucleotide)m

dAMP + phosphate + (ribonucleotide)n+m

Homo sapiens

-

-

1985

-

-

?

dATP + (ribonucleotide)n + (ribonucleotide)m

dAMP + phosphate + (ribonucleotide)n+m

Leishmania tarentolae

-

-

1997

-

-

?

dATP + (ribonucleotide)n + (ribonucleotide)m

dAMP + phosphate + (ribonucleotide)n+m

Leishmania tarentolae UC

-

-

1997

-

-

?

dATP + (ribonucleotide)n + (ribonucleotide)m

dAMP + phosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

at 20% the activity relative to ATP

1995

-

-

?

dATP + (ribonucleotide)n + (ribonucleotide)m

dAMP + phosphate + (ribonucleotide)n+m

Tequatrovirus T4

-

acts on single-stranded or double-stranded DNA molecules. Acts on very small pieces of ribonucleic acid, with 40mers being the probable upper size limit. The minimum size of the 5'-moiety is a ribonucleoside 3',5'-bisphosphate

1910

-

-

?

dATP + (ribonucleotide)n + (ribonucleotide)m

dAMP + phosphate + (ribonucleotide)n+m

Triticum aestivum

-

-

1984

-

-

?

additional information

?

-

Anabaena sp.

-

the group I intron from cyanobacterium Anabaena sp. catalyzes phosphodiester bond formation using a triphosphate on the 5'-terminal nucleotide, much like protein polymerases and engineered ribozymes. In the process, this ribozyme forms a unique circular RNA that incorporates the exogenous guanosine cofactor added during self-splicing

694311

-

-

?

additional information

?

-

Branchiostoma floridae

C3YGD8

the RNA ligase has a a strict requirement for RNA substrates with a 2'-phosphate terminus for the ligation of RNAs with 5'-phosphate and 3'-hydroxyl ends. RNA ligase forms a 2'-phosphomonoester-3',5'-phosphodiester junction

716756

-

-

?

additional information

?

-

Branchiostoma floridae

-

the RNA ligase has a a strict requirement for RNA substrates with a 2'-phosphate terminus for the ligation of RNAs with 5'-phosphate and 3'-hydroxyl ends. RNA ligase forms a 2'-phosphomonoester-3',5'-phosphodiester junction

716756

-

-

?

additional information

?

-

Escherichia coli

-

RtcA is able of cyclizing a 2'-phosphate RNA end in high yield. The rate of 2'-phosphate cyclization by RtcA is five orders of magnitude slower than 3'-phosphate cyclization, notwithstanding that RtcA binds with similar affinity to RNA3'p and RNA2'p substrates

728788

-

-

?

additional information

?

-

Methanothermobacter thermautotrophicus

-

enzyme does not discriminate between RNA and DNA for phosphodiester bond formation

694452

-

-

?

additional information

?

-

Methanothermobacter thermautotrophicus

-

intramolecular ligation of 5'-PO4 single-strand RNA to form a covalently closed circular RNA molecule through ligase-adenylylate and RNA-adenylylate intermediates AppRNA. At the optimal temperature of 65°C, AppRNA is predominantly ligated to a circular product. At 35°C, phosphodiester bond formation is suppressed and the majority of the AppRNA is deadenylylated

694452

-

-

?

additional information

?

-

Methanothermobacter thermautotrophicus

-

the enzyme catalyzes an adenylation reaction that is specific for ATP and either ssDNA or RNA. It does not require synthesis of a template strand for adenylation. To achieve quantitative DNA adenylation, single turnover reaction condition with substrate to enzyme ratio 1:1 should be used

728392

-

-

?

additional information

?

-

Methanothermobacter thermautotrophicus

-

the enzyme catalyzes formation of phosphodiester bonds between the 5'-phosphate and 3'-hydroxyl termini of single-stranded RNAs. It can also react with RNA with a 3'-phosphate end to generate a 2',3'-cyclic phosphate. The enzyme can additionally remove adenosine from the 3'-terminus of the RNA to produce 3'-deadenylated RNA

749330

-

-

?

additional information

?

-

Naegleria gruberi

-

the enzyme is unreactive with a 5'-32P-labeled single-strand 18-mer pDNA substrate

749277

-

-

?

additional information

?

-

Naegleria gruberi

-

the enzyme seals nicked 3'-OH/5'-PO4 duplexes in which the 3'-OH strand is RNA. The enzyme entails reaction with ATP to form a covalent enzyme-AMP intermediate, transfer of AMP to the nick 5'-PO4, and attack of the RNA 3'-OH on the adenylylated nick to form a 3'-5' phosphodiester

749277

-

-

?

additional information

?

-

Tequatrovirus T4

-

joins single-stranded DNA molecules much less efficiently. Many of them approximate a well-defined consensus sequence

2000

-

-

?

additional information

?

-

Tequatrovirus T4

-

efficient ligation of single-stranded DNAs and RNAs

653234

-

653234

?

additional information

?

-

Tequatrovirus T4

-

synthesizes circular hammerhead ribozymes from oligonucleotides, small RNA molecules resistant to circuarization by other means can be efficiently circularized on a preparative scale using a suitable DNA template

653369

-

653369

?

additional information

?

-

Tequatrovirus T4

-

no activity with alendronate nor pamidronate

673669

-

-

?

additional information

?

-

Tequatrovirus T4

-

T4 RNA ligase possesses nick-joining activity in RNA/DNA hybrids against junctional matches/mismatches complementary to the RNA strand as a ligation template. When a junctional mismatch is present at the 30-terminal of RNA probe, the nick-joining activity of T4Rnl2 is inhibited

713745

-

-

?

additional information

?

-

Triticum aestivum

-

RNA-stimulated exchange reaction between ATP and diphosphate

1984

-

-

?

additional information

?

-

Triticum aestivum

-

wheat RNA ligase can be dissected into three isolated domain enzymes that are responsible for its core ligase, 5'-kinase, and 2',3'-cyclic phosphate 3'-phosphodiesterase activities, respectively. A side reaction on 5'-tri/diphosphate RNAs is dependent on ATP, a 2'-phosphate-3'-hydroxyl end, and the ligase domain. Two RNA molecules having 5'-hydroxyl and 2',3'-cyclic monophosphate groups are ligated almost stoichiometrically after separate conversion of respective terminal phosphate states into reactive ones

714046

-

-

?

additional information

?

-

Triticum aestivum

-

wheat RNA ligase contains 5'-hydroxyl kinase, 2',3'-cyclic phosphate 3'-phosphodiesterase, and 5'-phosphate 2'-phosphate-3'-hydroxyl RNA ligase activities

714026

-

-

?