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Topic: Ligase


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In the News (Tue 16 Jul 19)

  
  DNA ligase - Wikipedia, the free encyclopedia
The mechanism of DNA ligase, esta bela porra, in connecting broken DNA strands is to form covalent phosphodiester bonds between 3' hydroxyl ends of one nucleotide with the 5' phosphate end of another.
DNA ligase I: ligates Okazaki fragments during lagging strand DNA replication and some recombinant fragments.
DNA ligase III: complexes with DNA repair protein XRCC1 to aid in sealing base excision mutations and recombinant fragments.
en.wikipedia.org /wiki/DNA_ligase   (477 words)

  
 Ligase - Wikipedia, the free encyclopedia
In biochemistry, a ligase (from the Latin verb ligāre — "to bind" or "to glue together") is an enzyme that can catalyse the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis of a small chemical group pendant to one of the larger molecules.
The common names of ligase enzymes often include the word "ligase", such as DNA ligase, an enzyme commonly used in molecular biology laboratories to join together DNA fragments.
Ligases are classified as EC 6 in the EC number classification of enzymes.
en.wikipedia.org /wiki/Ligase   (275 words)

  
 DNA Ligase: Structure, Mechanism, and Function -- Lehnman 186 (4166): 790 -- Science
Characterization of a Thermophilic ATP-Dependent DNA Ligase from the Euryarchaeon Pyrococcus horikoshii.
Characterization of a temperature-sensitive DNA ligase from Escherichia coli.
Characterization of an ATP-dependent DNA ligase from the thermophilic archaeon Methanobacterium thermoautotrophicum.
www.sciencemag.org /cgi/content/abstract/186/4166/790   (1080 words)

  
 Binding of Nucleotides by T4 DNA Ligase and T4 RNA Ligase: Optical Absorbance and Fluorescence Studies -- Cherepanov ...
T4 DNA ligase and RNA ligase were purchased from MBI Fermentas (Vilnus, Lithuania).
T4 DNA ligase was incubated both in the presence and the absence of 0.05 mg/ml BSA, at +4°C and +20°C. The enzyme was diluted in the reaction buffer to a final concentration of 1 U/ml (~6 nM).
versus 293 and 296 nm for RNA ligase).
www.biophysj.org /cgi/content/full/81/6/3545   (7081 words)

  
 DNA Ligase   (Site not responding. Last check: 2007-11-03)
DNA ligases catalyze formation of a phosphodiester bond between the 5' phosphate of one strand of DNA and the 3' hydroxyl of the another.
A DNA ligase from E. coli is also available, but is not commonly used.
Additional information on the use of T4 DNA ligase is presented in the section on DNA ligation.
arbl.cvmbs.colostate.edu /hbooks/genetics/biotech/enzymes/ligase.html   (139 words)

  
 Mapping and Use of a Sequence that Targets DNA Ligase I to Sites of DNA Replication In Vivo -- Cardoso et al. 139 (3): ...
ligase I with the affinity-purified anti-DNA ligase I rabbit antibodies
DNA ligase I with the affinity-purified rabbit antibodies.
I fused at the COOH terminus of the GFP.
www.jcb.org /cgi/content/full/139/3/579   (6984 words)

  
 Benzoate-Coenzyme A Ligase from Thauera aromatica: an Enzyme Acting in Anaerobic and Aerobic Pathways -- Schühle ...
Purification and characterization of benzoate-coenzyme A ligase and 2-aminobenzoate-coenzyme A ligases from a denitrifying Pseudomonas sp.
Benzoate-coenzyme A ligase, encoded by badA, is one of three ligases able to catalyze benzoyl-coenzyme A formation during anaerobic growth of Rhodopseudomonas palustris on benzoate.
Purification and characterization of phenylacetate-coenzyme A ligase from a denitrifying Pseudomonas sp., an enzyme involved in the anaerobic degradation of phenylacetate.
jb.asm.org /cgi/content/full/185/16/4920   (5078 words)

  
 DNA Ligation
T4 DNA ligase will also ligate fragments with blunt ends, although higher concentrations of the enzyme are usually recommended for this purpose.
However, ligase is active at a broad range of temperatures, and for routine purposes such as subcloning, convenience often dictates incubation time and temperature - ligations performed at 4C overnight or at room temperature for 30 minutes to a couple of hours usually work well.
DNA fragments generated by digestion of a plasmid with two restriction enzymes were incubated with different amounts of ligase for varying periods of time, then electrophoresed in 1% agarose.
arbl.cvmbs.colostate.edu /hbooks/genetics/biotech/enzymes/ligation.html   (373 words)

  
 LIGASE
LIGASE, The Long Island Group About Science and Education, is a consortial partnership using innovative academic year biology curricula, summer programs for teachers and students, and input from the biotechnology industry to educate students in current techniques in the growing field of biotechnology.
LIGASE, is a partnership encompassing SUNY Stony Brook, Nassau Community College, Suffolk County Community College, Uniondale High School, Brentwood High School and the Long Island High Technology Incubator.
The Goal of LIGASE is to educate a highly skilled work force for the growing biotechnology industry on Long Island.
www2.sunysuffolk.edu /gambier/biotechnologyl/newpage6.htm   (276 words)

  
 DNA ligase - Free net encyclopedia (via CobWeb/3.1 vn1.cs.wustl.edu)   (Site not responding. Last check: 2007-11-03)
The mechanism of DNA ligase in connecting broken DNA strands is to form covalent phosphodiester bonds between 3' hydroxyl ends of one nucleotide with the 5' phosphate end of another.
DNA ligase IV: complexes with DNA protein XRCC4.
For example, it is possible mix cut plasmids (with sticky ends), free-floating genes (with complementary sticky ends), and ligase to insert the gene into the plasmid.
www.netipedia.com.cob-web.org:8888 /index.php/DNA_ligase   (501 words)

  
 Characterization of a temperature-sensitive DNA ligase from Escherichia coli -- Lavesa-Curto et al. 150 (12): 4171 -- ...
Characterization of a temperature-sensitive DNA ligase from Escherichia coli -- Lavesa-Curto et al.
Modrich, P. and Lehman, I. Enzymatic characterization of a mutant of Escherichia coli with an altered DNA ligase.
Sriskanda, V., Schwer, B., Ho, C. and Shuman, S. Mutational analysis of Escherichia coli DNA ligase identifies amino acids required for nick-ligation in vitro and for in vivo complementation of the growth of yeast cells deleted for CDC9 and LIG4.
mic.sgmjournals.org /cgi/content/full/150/12/4171   (5006 words)

  
 Impact of DNA ligase IV on nonhomologous end joining pathways during class switch recombination in human cells -- ...
Impact of DNA ligase IV on nonhomologous end joining pathways during class switch recombination in human cells -- Pan-Hammarström et al.
Identification of a defect in DNA ligase IV in a radiosensitive leukaemia patient.
DNA ligase IV mutations identified in patients exhibiting developmental delay and immunodeficiency.
www.jem.org /cgi/content/full/201/2/189   (3577 words)

  
 T4 DNA Ligase, Cloned, EPICENTRE® Biotechnologies
T4 DNA Ligase is a commonly used ATP-dependent ligase for DNA cloning.
Following a ligation reaction, T4 DNA Ligase may be inactivated by incubation at 65°C for 10 minutes.
T4 DNA Ligase is available at concentrations of 2 Weiss Units/µl (134 Cohesive End Units/µl), and at a higher 10 Weiss Units/µl (670 Cohesive End Units/µl) for blunt-end ligation.
www.epibio.com /item.asp?ID=356&CatID=4&SubCatID=38   (453 words)

  
 In Vitro and In Vivo Interactions of DNA Ligase IV with a Subunit of the Condensin Complex -- Przewloka et al. 14 (2): ...
Although DNA ligase IV localized to punctate structures coincident with DNA staining, XRCC4 staining was present as a diffuse halo throughout the cell.
The relative abundance of DNA ligase IV and XRCC4 on mitotic chromosomes from colcemid-arrested cells and in untreated cell nuclear extracts.
DNA ligase IV from mitotic chromosome isolations displayed reduced mobility relative to that of nuclear extract, suggesting a possible posttranslational modification.
www.molbiolcell.org /cgi/content/full/14/2/685   (7490 words)

  
 Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ...
dimensions of the ligase footprint at a nick (24).
Weiss,B., Thompson,A. and Richardson,C.C. (1968) Enzymatic breakage and rejoining of deoxyribonucleic acid: properties of the enzyme–adenylate intermediate in the polynucleotide ligase reaction.
Sriskanda,V., Schwer,B., Ho,C.K. and Shuman,S. (1999) Mutational analysis of Escherichia coli DNA ligase identifies amino acids required for nick-ligation in vitro and for in vivo complementation of the growth of yeast cells deleted for CDC9 and LIG4.
nar.oxfordjournals.org /cgi/content/full/31/17/5090   (6704 words)

  
 InterPro: IPR005810 Succinyl-CoA ligase, alpha subunit
ATP-citrate lyase is a tetramer of identical subunits; Succinyl-CoA ligase (GDP-forming) (EC:6.2.1.4) [ 2 ] is a mitochondrial enzyme that catalyzes the substrate level phosphorylation step of the tricarboxylic acid cycle: the formation of succinyl-CoA from succinate with a concomitant hydrolysis of GTP to GDP and phosphate.
This enzyme is a dimer composed of an alpha and a beta subunits; Succinyl-CoA ligase (ADP-forming) (EC:6.2.1.5) [ 3 ] is a bacterial enzyme that during aerobic metabolism functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP.
This enzyme is a tetramer composed of two alpha and two beta subunits; and Malate-CoA ligase (EC:6.2.1.9) (malyl-CoA synthetase) [ 4 ], is a bacterial enzyme that forms malyl-CoA from malate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate.
www.ebi.ac.uk /interpro/IEntry?ac=IPR005810   (3361 words)

  
 DNA ligase I null mouse cells show normal DNA repair activity but altered DNA replication and reduced genome stability ...
DNA ligase I null mouse cells show normal DNA repair activity but altered DNA replication and reduced genome stability -- Bentley et al.
DNA ligase I is the key ligase for DNA replication in mammalian
ligase to compensate for DNA ligase I deficiency.
jcs.biologists.org /cgi/content/abstract/115/7/1551   (482 words)

  
 DNA ligase IV from a basidiomycete, Coprinus cinereus, and its expression during meiosis -- Namekawa et al. 149 (8): ...
DNA ligase IV from a basidiomycete, Coprinus cinereus, and its expression during meiosis -- Namekawa et al.
DNA ligase IV from a basidiomycete, Coprinus cinereus, and its expression during meiosis
West, C. E., Waterworth, W. M., Jiang, Q. and Bray, C. Arabidopsis DNA ligase IV is induced by gamma-irradiation and interacts with an Arabidopsis homologue of the double strand break repair protein XRCC4.
mic.sgmjournals.org /cgi/content/full/149/8/2119   (4847 words)

  
 DNA Ligase at Work - Medgadget - www.medgadget.com
It turns out that DNA ligase switches its configuration from an open form to circular-like shape to enclose the DNA during the repair, as seen in the picture.
The closed conformation of DNA ligase bound to DNA was imaged in a separate study previously reported by Ellenberger's group.
Ellenberger says that the challenge for the future is to study the molecular choreography of ligase, PCNA and DNA in the same experiment, which will require new methods of analyzing the SAXS data.
www.medgadget.com /archives/2006/10/dna_ligase_at_w.html   (349 words)

  
 Ligases: T4 DNA Ligases
The T4 DNA Ligase catalyzes the formation of a phosphodiester bond between juxtaposed 5'-phosphate and 3'-hydroxyl termini in duplex DNA or RNA with blunt or cohesive-end termini.
The T4 DNA Ligase binding to DNA may result in a band shift in agarose gels.
Rossi, R., et al., Functional characterization of the T4 DNA Ligase: a new insight into the mechanism of action, Nucleic Acids Res., 25, 2106-2113, 1997.
www.fermentas.com /catalog/modifyingenzymes/t4dnaligase.htm   (616 words)

  
 Structure-function analysis of yeast tRNA ligase -- WANG and SHUMAN 11 (6): 966 -- RNA
Englert, M. and Beier, H. Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins.
Phizicky, E.M., Consaul, S.A., Nehrke, K.W., and Abelson, J. Yeast tRNA ligase mutants are nonviable and accumulate tRNA splicing intermediates.
Pick, L. and Hurwitz, J. Purification of wheat germ RNA ligase: Characterization of a ligase-associated 5'-hydroxyl polynucleotide kinase activity.
www.rnajournal.org /cgi/content/full/11/6/966   (4975 words)

  
 Trevigen, Inc.
Human DNA Ligase IV/XRCC4 participates in the repair of DNA double-strand breaks in DNA via a direct nonhomologous end-joining (NHEJ) pathway.
DNA Ligase IV/XRCC4 exists as a tetramer containing two copies of each polypeptide with a molecular weight of approximately 300 kDa.
Lee, K.J., Huang, J., Takeda, Y., Dynan, W.S. DNA ligase IV and XRCC4 form a mixed tetramer that functions synergistically with other repair factors in a cell-free end-joining assay.
www.trevigen.com /dnaligase.php   (297 words)

  
 Role of DNA Ligase in the Illegitimate Recombination That Generates {{lambda}}bio-Transducing Phages in Escherichia ...
Role of DNA Ligase in the Illegitimate Recombination That Generates {{lambda}}bio-Transducing Phages in Escherichia coli -- Onda et al.
HL7 and HL48 are from the lysogen overexpressing DNA ligase,
DNA ligase is present only in low concentrations.
www.genetics.org /cgi/content/full/158/1/29   (3401 words)

  
 LIGASE - Long Island Group Advancing Science Education at Stony Brook University
LIGASE names Andrea Montalvo October 2006 Teacher of the Month (10/06)
Middle and high school students carry out summer research in our laboratories and work in the Biotechnology Teaching Center during the academic year.
Our vision is to build partnerships, attract talent, and make available innovative science offerings so that we continue to set a national standard for delivering science education for decades to come.
www.sunysb.edu /ligase   (170 words)

  
 Ligases: T4 RNA Ligase
The T4 RNA Ligase catalyzes the ATP-dependent intra- and intermolecular formation of phosphodiester bonds between 5'-phosphate and 3'-hydroxyl termini of oligonucleotides, single-stranded RNA and DNA.
Middleton, T., et al., Synthesis and purification of oligoribonucleotides using T4 RNA ligase and reverse-phase chromatography, Anal.
Brennan, C.A., et al., Using T4 RNA ligase with DNA substrates, Meth.
www.fermentas.com /catalog/modifyingenzymes/t4rnaligase.htm   (313 words)

  
 Requirement for XRCC4 and DNA Ligase IV in Alignment-based Gap Filling for Nonhomologous DNA End Joining in Vitro -- ...
(13), XRCC4 is stable in the absence of ligase IV.
Bryans M., Valenzano M. C., Stamato T. Absence of DNA ligase IV protein in XR-1 cells: evidence for stabilization by XRCC4.
Chen L., Trujillo K., Sung P., Tomkinson A. Interactions of the DNA ligase IV-XRCC4 complex with DNA ends and the DNA-dependent protein kinase.
cancerres.aacrjournals.org /cgi/content/full/63/1/22   (2380 words)

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