Reference on EC 6.5.1.3 - RNA ligase (ATP)
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REF. 
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Maunders, M.J.
DNA and RNA ligases (EC 6.5.1.1, EC 6.5.1.2, and EC 6.5.1.3)
Methods Mol. Biol.
16
213-230
1993
Tequatrovirus T4
Pick, L.; Hurwitz, J.
Purification of wheat germ RNA ligase. I. Characterization of a ligase-associated 5'-hydroxyl polynucleotide kinase activity
J. Biol. Chem.
261
6684-6693
1986
Triticum aestivum
Pick, L.; Furneaux, H.; Hurwitz, J.
Purification of wheat germ RNA ligase. II. Mechanism of action of wheat germ RNA ligase
J. Biol. Chem.
261
6694-6704
1986
Triticum aestivum
Perkins, K.K.; Furneaux, H.; Hurwitz, J.
Isolation and characterization of an RNA ligase from HeLa cells
Proc. Natl. Acad. Sci. USA
82
684-688
1985
Homo sapiens
Rand, K.N.; Gait, M.J.
Sequence and cloning of bacteriophage T4 gene 63 encoding RNA ligase and tail fibre attachment activities
EMBO J.
3
397-402
1984
Tequatrovirus T4
Furneaux, H.; Pick, L.; Hurwitz, J.
Isolation and characterization of RNA ligase from wheat germ
Proc. Natl. Acad. Sci. USA
80
3933-3937
1983
Triticum aestivum
Gegenheimer, P.; Gabius, H.J.; Peebles, C.L.; Abelson, J.
An RNA ligase from wheat germ which participates in transfer RNA splicing in vitro
J. Biol. Chem.
258
8365-8373
1983
Triticum aestivum
Mei-Hao, H.; Wang, A.; Hui-Fen, H.
Purification of T4 RNA ligase by dextran blue-Sepharose 4B affinity chromatography
Anal. Biochem.
125
1-5
1982
Tequatrovirus T4
Dolganov, G.M.; Chestukhin, A.V.; Shemyakin, M.
A new procedure for the simultaneous large-scale purification of bacteriophage-T4-induced polynucleotide kinase, DNA ligase, RNA ligase and DNA polymerase
Eur. J. Biochem.
114
247-254
1981
Tequatrovirus T4
Konarska, M.; Filipowicz, W.; Domdey, H.; Gross, H.J.
Formation of a 2'-phosphomonoester, 3',5'-phosphodiester linkage by a novel RNA ligase in wheat germ
Nature
293
112-116
1981
Triticum aestivum
Moseman McCoy, M.I.; Lubben, T.H.; Gumport, R.I.
The Purification of nuclease-free T4-RNA ligase
Biochim. Biophys. Acta
562
149-161
1979
Tequatrovirus T4
Sugiura, M.; Suzuki, M.; Ohtsuka, E.; Nishikawa, S.; Uemura, H.; Ikehara, M.
Purification of T4 RNA ligase by 2',5'-ADP Sepharose chromatography
FEBS Lett.
97
73-76
1979
Tequatrovirus T4
Last, J.A.; Anderson, W.F.
Purification and properties of bacteriophage T4-induced RNA ligase
Arch. Biochem. Biophys.
174
167-176
1976
Tequatrovirus T4
Silber, R.; Malathi, V.G.; Hurwitz, J.
Purification and properties of bacteriophage T4-induced RNA ligase
Proc. Natl. Acad. Sci. USA
69
3009-3013
1972
Tequatrovirus T4
Rusche, L.N.; Cruz-Reyes, J.; Piller, K.J.; Sollner-Webb, B.
Purification of a functional enzymatic editing complex from Trypanosoma brucei mitochondria
EMBO J.
16
4069-4081
1997
Trypanosoma brucei
Bakalara, N.; Simpson, A.M.; Simpson, L.
The Leishmania kinetoplast-mitochondrion contains terminal uridylyltransferase and RNA ligase activities
J. Biol. Chem.
264
18679-18686
1989
Leishmania tarentolae
Juodka, B.; Labeikyte, D.
Inhibition of the first stage of RNA ligase reaction by ATP analogues
Nucleosides Nucleotides
10
367-370
1991
Tequatrovirus T4
-
Pick, L.; Furneaux, H.M.; Hurwitz, J.
Purification and characterization of wheat germ RNA ligase and associated activities
Methods Enzymol.
181
480-499
1990
Triticum aestivum
Harada, K.; Orgel, L.E.
In vitro selection of optimal substrates for T4 RNA ligase
Proc. Natl. Acad. Sci. USA
90
1576-1579
1993
Tequatrovirus T4
Iuoda, B.A.; Labeikite, D.; Sasnauskene, S.I.
Substrate specificity of T4 RNA-ligase: the role of a purine nucleotide base in forming a covalent AMP-RNA ligase complex
Biokhimiia
58
857-865
1993
Tequatrovirus T4
Bergman, N.H.; Johnston, W.K.; Bartel, D.P.
Kinetic framework for ligation by an efficient RNA ligase ribozyme
Biochemistry
39
3115-3123
2000
synthetic construct
Glasner, M.E.; Bergman, N.H.; Bartel, D.P.
Metal ion requirements for structure and catalysis of an RNA ligase ribozyme
Biochemistry
41
8103-8112
2002
synthetic construct
Wang, Q.S.; Unrau, P.J.
Purification of histidine-tagged T4 RNA ligase from E. coli
Biotechniques
33
1256-1260
2002
Tequatrovirus T4
Huang, C.E.; Cruz-Reyes, J.; Zhelonkina, A.G.; O'Hearn, S.; Wirtz, E.; Sollner-Webb, B.
Roles for ligases in the RNA editing complex of Trypanosoma brucei: band IV is needed for U-deletion and RNA repair
EMBO J.
20
4694-4703
2001
Trypanosoma brucei
Atencia, E.A.; Madrid, O.; Gunther Sillero, M.A.; Sillero, A.
T4 RNA ligase catalyzes the synthesis of dinucleoside polyphosphates
Eur. J. Biochem.
261
802-811
1999
Tequatrovirus T4
Atencia, E.A.; Montes, M.; Gunther Sillero, M.A.; Sillero, A.
Several dinucleoside polyphosphates are acceptor substrates in the T4 RNA ligase catalyzed reaction
Eur. J. Biochem.
267
1707-1714
2000
Tequatrovirus T4
Piller, K.J.; Rusche, L.N.; Sollner-Webb, B.
Trypanosoma brucei RNA editing. A full round of uridylate insertional editing in vitro mediated by endonuclease and RNA ligase
J. Biol. Chem.
271
4613-4619
1996
Trypanosoma brucei
Cherepanov, A.V.; de Vries, S.
Kinetic mechanism of the Mg2+-dependent nucleotidyl transfer catalyzed by T4 DNA and RNA ligases
J. Biol. Chem.
277
1695-1704
2002
Tequatrovirus T4
Yin, S.; Ho, C.K.; Shuman, S.
Structure-function analysis of T4 RNA ligase 2
J. Biol. Chem.
278
17601-17608
2003
Tequatrovirus T4
Wang, L.K.; Ho, C.K.; Pei, Y.; Shuman, S.
Mutational analysis of bacteriophage T4 RNA ligase 1. Different functional groups are required for the nucleotidyl transfer and phosphodiester bond formation steps of the ligation reaction
J. Biol. Chem.
278
29454-29462
2003
Tequatrovirus T4
Cruz-Reyes, J.; Zhelonkina, A.G.; Huang, C.E.; Sollner-Webb, B.
Distinct functions of two RNA ligases in active Trypanosoma brucei RNA editing complexes
Mol. Cell. Biol.
22
4652-4660
2002
Trypanosoma brucei
Nishigaki, K.; Taguchi, K.; Kinoshita, Y.; Aita, T.; Husimi, Y.
Y-ligation: an efficient method for ligating single-stranded DNAs and RNAs with T4 RNA ligase
Mol. Divers.
4
187-190
1998
Tequatrovirus T4
Ekland, E.H.; Bartel, D.P.
The secondary structure and sequence optimization of an RNA ligase ribozyme
Nucleic Acids Res.
23
3231-3238
1995
synthetic construct
Wang, L.; Ruffner, D.E.
Oligoribonucleotide circularization by 'template-mediated' ligation with T4 RNA ligase: synthesis of circular hammerhead ribozymes
Nucleic Acids Res.
26
2502-2504
1998
Tequatrovirus T4
Blondal, T.; Hjorleifsdottir, S.H.; Fridjonsson, O.F.; Aevarsson, A.; Skirnisdottir, S.; Hermannsdottir, A.G.; Hreggvidsson, G.O.; Smith, A.V.; Kristjansson, J.K.
Discovery and characterization of a thermostable bacteriophage RNA ligase homologous to T4 RNA ligase 1
Nucleic Acids Res.
31
7247-7254
2003
Rhodothermus phage RM378
Ho, C.K.; Shuman, S.
Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains
Proc. Natl. Acad. Sci. USA
99
12709-12714
2002
Tequatrovirus T4
McManus, M.T.; Shimamura, M.; Grams, J.; Hajduk, S.L.
Identification of candidate mitochondrial RNA editing ligases from Trypanosoma brucei
RNA
7
167-175
2001
Trypanosoma brucei
Ekland, E.H.; Szostak, J.W.; Bartel, D.P.
Structurally complex and highly active RNA ligases derived from random RNA sequences
Science
269
364-370
1995
synthetic construct
Schnaufer, A.; Panigrahi, A.K.; Panicucci, B.; Igo, R.P., Jr.; Wirtz, E.; Salavati, R.; Stuart, K.
An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei
Science
291
2159-2162
2001
Trypanosoma brucei
Ho, C.K.; Wang, L.K.; Lima, C.D.; Shuman, S.
Structure and mechanism of RNA ligase
Structure
12
327-339
2004
Tequatrovirus T4 (P32277)
Yin, S.; Kiong Ho, C.; Miller, E.S.; Shuman, S.
Characterization of bacteriophage KVP40 and T4 RNA ligase 2
Virology
319
141-151
2004
Tequatrovirus T4, Vibrio phage KVP40
Nandakumar, J.; Ho, C.K.; Lima, C.D.; Shuman, S.
RNA substrate specificity and structure-guided mutational analysis of bacteriophage T4 RNA ligase 2
J. Biol. Chem.
279
31337-31347
2004
Tequatrovirus T4
Martins, A.; Shuman, S.
An RNA ligase from Deinococcus radiodurans
J. Biol. Chem.
279
50654-50661
2004
Deinococcus radiodurans
Deng, J.; Schnaufer, A.; Salavati, R.; Stuart, K.D.; Hol, W.G.
High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei:RNA editing ligase 1
J. Mol. Biol.
343
601-613
2004
Trypanosoma brucei
Blondal, T.; Thorisdottir, A.; Unnsteinsdottir, U.; Hjorleifsdottir, S.; Aevarsson, A.; Ernstsson, S.; Fridjonsson, O.H.; Skirnisdottir, S.; Wheat, J.O.; Hermannsdottir, A.G.; Sigurdsson, S.T.; Hreggvidsson, G.O.; Smith, A.V.; Kristjansson, J.K.
Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties
Nucleic Acids Res.
33
135-142
2005
Phage TS2126
Gao, G.; Simpson, A.M.; Kang, X.; Rogers, K.; Nebohacova, M.; Li, F.; Simpson, L.
Functional complementation of Trypanosoma brucei RNA in vitro editing with recombinant RNA ligase
Proc. Natl. Acad. Sci. USA
102
4712-4717
2005
Leishmania tarentolae, Trypanosoma brucei
Nandakumar, J.; Shuman, S.; Lima, C.D.
RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward
Cell
127
71-84
2006
Tequatrovirus T4 (P32277)
Sillero, M.A.; de Diego, A.; Silles, E.; Perez-Zuniga, F.; Sillero, A.
Synthesis of bisphosphonate derivatives of ATP by T4 RNA ligase
FEBS Lett.
580
5723-5727
2006
Tequatrovirus T4
El Omari, K.; Ren, J.; Bird, L.E.; Bona, M.K.; Klarmann, G.; LeGrice, S.F.; Stammers, D.K.
Molecular architecture and ligand recognition determinants for T4 RNA ligase
J. Biol. Chem.
281
1573-1579
2006
Tequatrovirus T4
Wang, L.K.; Schwer, B.; Englert, M.; Beier, H.; Shuman, S.
Structure-function analysis of the kinase-CPD domain of yeast tRNA ligase (Trl1) and requirements for complementation of tRNA splicing by a plant Trl1 homolog
Nucleic Acids Res.
34
517-527
2006
Saccharomyces cerevisiae
Raymond, A.; Shuman, S.
Deinococcus radiodurans RNA ligase exemplifies a novel ligase clade with a distinctive N-terminal module that is important for 5-PO4 nick sealing and ligase adenylylation but dispensable for phosphodiester formation at an adenylylated nick
Nucleic Acids Res.
35
839-849
2007
Deinococcus radiodurans
Stark, M.R.; Pleiss, J.A.; Deras, M.; Scaringe, S.A.; Rader, S.D.
An RNA ligase-mediated method for the efficient creation of large, synthetic RNAs
RNA
12
2014-2019
2006
Tequatrovirus T4
Wang, L.K.; Nandakumar, J.; Schwer, B.; Shuman, S.
The C-terminal domain of T4 RNA ligase 1 confers specificity for tRNA repair
RNA
13
1235-1244
2007
Tequatrovirus T4
Robertson, M.P.; Scott, W.G.
The structural basis of ribozyme-catalyzed RNA assembly
Science
315
1549-1553
2007
Enterobacteria phage L1
Vicens, Q.; Cech, T.R.
A natural ribozyme with 3,5 RNA ligase activity
Nat. Chem. Biol.
5
97-99
2009
Anabaena sp.
Torchia, C.; Takagi, Y.; Ho, C.K.
Archaeal RNA ligase is a homodimeric protein that catalyzes intramolecular ligation of single-stranded RNA and DNA
Nucleic Acids Res.
36
6218-6227
2008
Methanothermobacter thermautotrophicus
Nelissen, F.H.; van Gammeren, A.J.; Tessari, M.; Girard, F.C.; Heus, H.A.; Wijmenga, S.S.
Multiple segmental and selective isotope labeling of large RNA for NMR structural studies
Nucleic Acids Res.
36
e89
2008
Tequatrovirus T4
Amaro, R.E.; Schnaufer, A.; Interthal, H.; Hol, W.; Stuart, K.D.; McCammon, J.A.
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei
Proc. Natl. Acad. Sci. USA
105
17278-17283
2008
Trypanosoma brucei (P86927), Trypanosoma brucei
Sillero, M.A.; de Diego, A.; Tavares, J.E.; Silva, J.A.; Perez-Zuniga, F.J.; Sillero, A.
Synthesis of ATP derivatives of compounds of the mevalonate pathway (isopentenyl di- and triphosphate; geranyl di- and triphosphate, farnesyl di- and triphosphate, and dimethylallyl diphosphate) catalyzed by T4 RNA ligase, T4 DNA ligase and other ligases
Biochem. Pharmacol.
78
335-343
2009
Tequatrovirus T4
Swift, R.V.; Amaro, R.E.
Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms
Expert Opin. Drug Discov.
4
1281-1294
2009
Trypanosoma brucei
Park, K.; Choi, B.R.; Kim, Y.S.; Shin, S.; Hah, S.S.; Jung, W.; Oh, S.; Kim, D.E.
Detection of single-base mutation in RNA using T4 RNA ligase-based nick-joining or DNAzyme-based nick-generation
Anal. Biochem.
414
303-305
2011
Tequatrovirus T4
Makino, S.; Sawasaki, T.; Endo, Y.; Takai, K.
In vitro dissection revealed that the kinase domain of wheat RNA ligase is physically isolatable from the flanking domains as a non-overlapping domain enzyme
Biochem. Biophys. Res. Commun.
397
762-766
2010
Triticum aestivum
Makino, S.; Sawasaki, T.; Endo, Y.; Takai, K.
Use of domain enzymes from wheat RNA ligase for in vitro preparation of RNA molecules
Biochem. Biophys. Res. Commun.
404
1050-1054
2011
Triticum aestivum
Durrant, J.D.; Hall, L.; Swift, R.V.; Landon, M.; Schnaufer, A.; Amaro, R.E.
Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1
PLoS Negl. Trop. Dis.
4
e803
2010
Trypanosoma brucei (P86927), Trypanosoma brucei
Englert, M.; Sheppard, K.; Gundllapalli, S.; Beier, H.; Soell, D.
Branchiostoma floridae has separate healing and sealing enzymes for 5'-phosphate RNA ligation
Proc. Natl. Acad. Sci. USA
107
16834-16839
2010
Branchiostoma floridae (C3YGD8), Branchiostoma floridae
Zhelkovsky, A.M.; McReynolds, L.A.
Simple and efficient synthesis of 5' pre-adenylated DNA using thermostable RNA ligase
Nucleic Acids Res.
39
e117
2011
Methanothermobacter thermautotrophicus
Chen, Y.R.; Zheng, Y.; Liu, B.; Zhong, S.; Giovannoni, J.; Fei, Z.
A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters
Plant Methods
8
41
2012
Escherichia coli
Das, U.; Shuman, S.
2-Phosphate cyclase activity of RtcA: a potential rationale for the operon organization of RtcA with an RNA repair ligase RtcB in Escherichia coli and other bacterial taxa
RNA
19
1355-1362
2013
Escherichia coli
Chauleau, M.; Shuman, S.
Kinetic mechanism of nick sealing by T4 RNA ligase 2 and effects of 3-OH base mispairs and damaged base lesions
RNA
19
1840-1847
2013
Tequatrovirus T4
Moreira, S.; Noutahi, E.; Lamoureux, G.; Burger, G.
Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2
BMC Struct. Biol.
15
20
2015
Diplonema papillatum (A0A0P0IR96), Diplonema papillatum
Desai, K.K.; Cheng, C.L.; Bingman, C.A.; Phillips, G.N.; Raines, R.T.
A tRNA splicing operon Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation
Nucleic Acids Res.
42
3931-3942
2014
Pyrococcus horikoshii
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
Nucleic Acids Res.
44
2337-2347
2016
Methanothermobacter thermautotrophicus (O27289), Methanothermobacter thermautotrophicus, Methanothermobacter thermautotrophicus ATCC 29096 (O27289)
Burroughs, A.M.; Aravind, L.
RNA damage in biological conflicts and the diversity of responding RNA repair systems
Nucleic Acids Res.
44
8525-8555
2016
Tequatrovirus T4 (P32277)
Unciuleac, M.C.; Goldgur, Y.; Shuman, S.
Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase
Proc. Natl. Acad. Sci. USA
112
13868-13873
2015
Naegleria gruberi
Unciuleac, M.C.; Shuman, S.
Characterization of a novel eukaryal nick-sealing RNA ligase from Naegleria gruberi
RNA
21
824-832
2015
Naegleria gruberi
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