Kinetic framework for ligation by an efficient RNA ligase ribozyme

Bergman, N.H.; Johnston, W.K.; Bartel, D.P.; Biochemistry 39, 3115-3123 (2000)

 show all sequences of 6.5.1.3

Data extracted from this reference:

Organism
Organism Primary Accession No. (UniProt) Commentary Textmining
synthetic construct
-
 isolated from random sequences, pool of random sequences based on their ability to join a substrate oligonucleotide to their own 5'-terminus
-
Substrates and Products (Substrate)
Substrates Commentary Substrates Literature (Substrates) Organism Products Commentary (Products) Literature (Products) Organism (Products) Reversibility
ATP + (ribonucleotide)n + (ribonucleotide)m 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 synthetic construct AMP + diphosphate + (ribonucleotide)n+m
-
 649963 synthetic construct ?
ATP + RNA + 5'-aaCCAGUC DNA-RNA hybrid 649963 synthetic construct AMP + diphosphate + ?
-
 649963 synthetic construct ?
Turnover Number [1/s]
Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Commentary Organism Structure
0.05
-
 (RNA)n pH 6.0, 22°C, multiple-turnover derivatives 210t and 207t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
0.266
-
 (RNA)n pH 8.0, 22°C, multiple-turnover derivative 207t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
0.583
-
 (RNA)n pH 9.0, 22°C, multiple-turnover derivative 207t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
2.33
-
 (RNA)n pH 8.0, 22°C, multiple-turnover derivative 210t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
2.94
-
 (RNA)n pH 8.0, 22°C, multiple-turnover derivative 210t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
6
-
 (RNA)n pH 9.0, 22°C, multiple-turnover derivative 210t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
6.08
-
 (RNA)n pH 9.0, 22°C, multiple-turnover derivative 207t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
Substrates and Products (Substrate) (protein specific)
Substrates Commentary Substrates Literature (Substrates) Organism Products Commentary (Products) Literature (Products) Organism (Products) Reversibility
ATP + (ribonucleotide)n + (ribonucleotide)m 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 synthetic construct AMP + diphosphate + (ribonucleotide)n+m
-
 649963 synthetic construct ?
ATP + RNA + 5'-aaCCAGUC DNA-RNA hybrid 649963 synthetic construct AMP + diphosphate + ?
-
 649963 synthetic construct ?
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Commentary Organism Structure
0.05
-
 (RNA)n pH 6.0, 22°C, multiple-turnover derivatives 210t and 207t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
0.266
-
 (RNA)n pH 8.0, 22°C, multiple-turnover derivative 207t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
0.583
-
 (RNA)n pH 9.0, 22°C, multiple-turnover derivative 207t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
2.33
-
 (RNA)n pH 8.0, 22°C, multiple-turnover derivative 210t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
2.94
-
 (RNA)n pH 8.0, 22°C, multiple-turnover derivative 210t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
6
-
 (RNA)n pH 9.0, 22°C, multiple-turnover derivative 210t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct
6.08
-
 (RNA)n pH 9.0, 22°C, multiple-turnover derivative 207t, engineered by changing the arrangement of the base pairs in the P2 stem synthetic construct

See also following references to EC number 6.5.1.3 (sorted by year of publication):
No.1st authorPub
Med		titleorganimsjournalvolumepagesyearActivating CompoundApplicationCloned(Commentary)Crystallization (Commentary)EngineeringGeneral StabilityInhibitorsKM Value [mM]LocalizationMetals/IonsMolecular Weight [Da]Natural Substrates/ Products (Substrates)Organic Solvent StabilityOrganismOxidation StabilityPosttranslational ModificationPurification (Commentary)ReactionRenatured (Commentary)Source TissueSpecific Activity [micromol/min/mg]Storage StabilitySubstrates and Products (Substrate)SubunitsTemperature Optimum [°C]Temperature Range [°C]Temperature Stability [°C]Turnover Number [1/s]pH OptimumpH RangepH StabilityCofactorKi Value [mM]pI ValueIC50 ValueActivating Compound (protein specific)Application (protein specific)Cloned(Commentary) (protein specific)Cofactor (protein specific)Crystallization (Commentary) (protein specific)Engineering (protein specific)General Stability (protein specific)IC50 Value (protein specific)Inhibitors (protein specific)Ki Value [mM] (protein specific)KM Value [mM] (protein specific)Localization (protein specific)Metals/Ions (protein specific)Molecular Weight [Da] (protein specific)Natural Substrates/ Products (Substrates) (protein specific)Organic Solvent Stability (protein specific)Oxidation Stability (protein specific)Posttranslational Modification (protein specific)Purification (Commentary) (protein specific)Renatured (Commentary) (protein specific)Source Tissue (protein specific)Specific Activity [micromol/min/mg] (protein specific)Storage Stability (protein specific)Substrates and Products (Substrate) (protein specific)Subunits (protein specific)Temperature Optimum [°C] (protein specific)Temperature Range [°C] (protein specific)Temperature Stability [°C] (protein specific)Turnover Number [1/s] (protein specific)pH Optimum (protein specific)pH Range (protein specific)pH Stability (protein specific)pI Value (protein specific)ExpressionGeneral InformationGeneral Information (protein specific)Expression (protein specific)KCat/KM [mM/s]KCat/KM [mM/s] (protein specific)
713745ParkDetection of single-base mutat ...Enterobacteria phage T4Anal. Biochem.414303-3052011-------------2--------1-----------------------------------1---------------
714046MakinoUse of domain enzymes from whe ...Triticum aestivumBiochem. Biophys. Res. Commun.4041050-10542011-------------3--------2-----------------------------------2---------------
714026MakinoIn vitro dissection revealed t ...Triticum aestivumBiochem. Biophys. Res. Commun.397762-7662010-------------4--------2-----------------------------------2---------------
716670DurrantNovel naphthalene-based inhibi ...Trypanosoma bruceiPLoS Negl. Trop. Dis.4e8032010--1---8------3--1-----1-----------4--1----48---------1----1----------11---
716756EnglertBranchiostoma floridae has sep ...Branchiostoma floridaeProc. Natl. Acad. Sci. USA10716834-168392010----1--------3--------2-----------------1-----------------2----------11---
694311VicensA natural ribozyme with 3,5 RN ...Anabaena sp.Nat. Chem. Biol.597-992009-----------1-3--------1--------------------------1--------1---------------
707449SilleroSynthesis of ATP derivatives o ...Enterobacteria phage T4Biochem. Pharmacol.78335-3432009-------7-----1------7-7----7-----------------7----------7-7----7--------77
708449SwiftDiscovery and design of DNA an ...Trypanosoma bruceiExpert Opin. Drug Discov.41281-12942009------1------2-----------------------------1------------------------------
694452TorchiaArchaeal RNA ligase is a homod ...Methanothermobacter thermautotrophicusNucleic Acids Res.366218-62272008--1-1--------4--------6211-----------1--1-----------------6211------------
694461NelissenMultiple segmental and selecti ...Enterobacteria phage T4Nucleic Acids Res.36e892008-1-----------4----------------------1-------------------------------------
694881AmaroDiscovery of drug-like inhibit ...Trypanosoma bruceiProc. Natl. Acad. Sci. USA10517278-172832008---1--4------5-------------------------1---4------------------------------
676230RaymondDeinococcus radiodurans RNA li ...Deinococcus radioduransNucleic Acids Res.35839-8492007----22--------3--------------------------22---------------------------------
677101WangThe C-terminal domain of T4 RN ...Enterobacteria phage T4RNA131235-12442007----6--------2--------1-----------------6-----------------1---------------
677128RobertsonThe structural basis of ribozy ...Enterobacteria phage L1Science3151549-15532007---1-----1-1-1--------1----------------1-------1-1--------1---------------
672949NandakumarRNA ligase structures reveal t ...Enterobacteria phage T4Cell12771-842006---1---------2--1----------------------1-------------1--------------------
673669SilleroSynthesis of bisphosphonate de ...Enterobacteria phage T4FEBS Lett.5805723-57272006-------3-----1--------4----3-----------------3------------4----3----------
674568El OmariMolecular architecture and lig ...Enterobacteria phage T4J. Biol. Chem.2811573-15792006--11-----1---3--1--------------------1-1-------1-----1--------------------
676215WangStructure-function analysis of ...Saccharomyces cerevisiaeNucleic Acids Res.34517-5272006--1-23------1-4--------1--------------1--23--------1--------1---------------
677096StarkAn RNA ligase-mediated method ...Enterobacteria phage T4RNA122014-20192006-1-----------1----------------------1-------------------------------------
662976BlondalIsolation and characterization ...Phage TS2126Nucleic Acids Res.33135-1422005-11---12-2---5--1-----1-112-11------11-----1-2-2-----1----1-112-11--------
663245GaoFunctional complementation of ...Leishmania tarentolae, Trypanosoma bruceiProc. Natl. Acad. Sci. USA1024712-47172005--2----------4--------2--------------2--------------------2---------------
653915HoStructure and mechanism of RNA ...Enterobacteria phage T4Structure12327-3392004--11-------1-4--1-----1-----2--------1-1---------1---1----1-----2---------
654015YinCharacterization of bacterioph ...Enterobacteria phage T4, Vibrio phage KVP40Virology319141-1512004--1-------12-5--1-----31----11-------1----------12---1----31----11--------
662241NandakumarRNA substrate specificity and ...Enterobacteria phage T4J. Biol. Chem.27931337-313472004----31----2---3--------1-----------------31------2----------1---------------
662304MartinsAn RNA ligase from Deinococcus ...Deinococcus radioduransJ. Biol. Chem.27950654-506612004----5--------3--------1-----------------5-----------------1---------------
662636DengHigh resolution crystal struct ...Trypanosoma bruceiJ. Mol. Biol.343601-6132004--11-----1-1-4--1-----2--------------1-1-------1-1---1----2---------------
652387YinStructure-function analysis of ...Enterobacteria phage T4J. Biol. Chem.27817601-176082003--1-13------1-2--1-----2-----1--------1--13--------1---1----2-----1---------
652429WangMutational analysis of bacteri ...Enterobacteria phage T4J. Biol. Chem.27829454-294622003--1-31------1-3--1-----1--------------1--31--------1---1----1---------------
653392BlondalDiscovery and characterization ...Rhodothermus phage RM378Nucleic Acids Res.317247-72542003--1---1--211-4--1-----1-1-1-2--------1-----1---211---1----1-1-1-2---------
650172GlasnerMetal ion requirements for str ...synthetic constructBiochemistry418103-81122002--1---10--3-1-2--1-----2------1-------1-----10---3-1---1----2------1--------
650653WangPurification of histidine-tagg ...Enterobacteria phage T4Biotechniques331256-12602002--1--------1-2--1-----1--------------1-----------1---1----1---------------
652246CherepanovKinetic mechanism of the Mg2+- ...Enterobacteria phage T4J. Biol. Chem.2771695-17042002---------1-1-2--1-----2------------------------1-1---1----2---------------
653217Cruz-ReyesDistinct functions of two RNA ...Trypanosoma bruceiMol. Cell. Biol.224652-46602002--------1-11-1--1-----2-----------------------1-11---1----2---------------
653679HoBacteriophage T4 RNA ligase 2 ...Enterobacteria phage T4Proc. Natl. Acad. Sci. USA9912709-127142002--1-6-----11-4--1-----2-----21-------1--6-------11---1----2-----21--------
650982HuangRoles for ligases in the RNA e ...Trypanosoma bruceiEMBO J.204694-47032001--1-2---1--1-3--------2--------------1--2-----1--1--------2---------------
653869McManusIdentification of candidate mi ...Trypanosoma bruceiRNA7167-1752001--1-----1-21-1--1-----2--------------1--------1-21---1----2---------------
653889SchnauferAn RNA ligase essential for RN ...Trypanosoma bruceiScience2912159-21622001-11-----1--1-3--1--1--2-------------11--------1--1---1-1--2---------------
649963BergmanKinetic framework for ligation ...synthetic constructBiochemistry393115-31232000-------------2--------2----7------------------------------2----7----------
651061AtenciaSeveral dinucleoside polyphosp ...Enterobacteria phage T4Eur. J. Biochem.2671707-17142000-------2--11-2--1-----2----------------------2--11---1----2---------------
651051AtenciaT4 RNA ligase catalyzes the sy ...Enterobacteria phage T4Eur. J. Biochem.261802-8111999------1----1-1------1-6----211-------------1-----1------1-6----211--------
653234NishigakiY-ligation: an efficient metho ...Enterobacteria phage T4Mol. Divers.4187-1901998-----------1-2-----1--2--------------------------1-----1--2---------------
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1996RuschePurification of a functional e ...Trypanosoma bruceiEMBO J.164069-40811997--------1----3--1-----11----------------------1------1----11--------------
651858PillerTrypanosoma brucei RNA editing ...Trypanosoma bruceiJ. Biol. Chem.2714613-46191996--------1--1-3--------2-----------------------1--1--------2---------------
653368EklandThe secondary structure and se ...synthetic constructNucleic Acids Res.233231-32381995-----------1-2--------1--------------------------1--------1---------------
653882EklandStructurally complex and highl ...synthetic constructScience269364-3701995-------1---1-1--------1----2-----------------1---1--------1----2----------
1910MaundersDNA and RNA ligases (EC 6.5.1. ...Enterobacteria phage T4Methods Mol. Biol.16213-2301993---------11--1-------12------------------------11--------12---------------
2000HaradaIn vitro selection of optimal ...Enterobacteria phage T4Proc. Natl. Acad. Sci. USA901576-15791993-------------1--------2-----------------------------------2---------------
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1998Juodka-Inhibition of the first stage ...Enterobacteria phage T4Nucleosides Nucleotides10367-3701991------8------1--------1--------------------8--------------1---------------
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1985PerkinsIsolation and characterization ...Homo sapiensProc. Natl. Acad. Sci. USA82684-6881985------1--1---2--1--1112--------------------1---1-----1-1112---------------
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1991KonarskaFormation of a 2'-phosphomonoe ...Triticum aestivumNature293112-1161981-------------3-----1--1--------------------------------1--1---------------
1992Moseman McCoyThe Purification of nuclease-f ...Enterobacteria phage T4Biochim. Biophys. Acta562149-1611979-------------3-----11-11-------------------------------11-11--------------
1993SugiuraPurification of T4 RNA ligase ...Enterobacteria phage T4FEBS Lett.9773-761979------1------1--1--11-1--------------------1---------1-11-1---------------
1994LastPurification and properties of ...Enterobacteria phage T4Arch. Biochem. Biophys.174167-1761976----------1--1-------111------------------------1--------111--------------
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