Biomaterial Database

Agrobacterium tumefaciens RNA polymerase: a new purification procedure and a study of the stable binding sites on homologous deoxyribonucleic acid. 1981

M Cardarelli, and M Pomponi, and G Risuleo, and E Di Mauro

RNA polymerase (RNA nucleotidyltransferase, EC 2.7.7.6) of Agrobacterium tumefaciens has been purified according to a fast and efficient procedure. The method involves only two chromatographic steps and yields a highly active enzyme. The RNA polymerase was studied with respect to the ability to bind its homologous genome. A. tumefaciens deoxyribonucleic acid (DNA) binds the enzyme even when fragmented at undergenic size (300 base pairs). The general binding is unspecific and very labile at low concentrations of heparin (0.66 micrograms/mL). The number and distribution of the stable binding sites, class A sites [Hinkle, D., & Chamberlin, M. J. (1972) J. Mol. Biol. 70, 157-185], have been calculated from the heparin-induced dissociation kinetics of binary complexes formed between the enzyme and DNA fragments of various sizes. A total of 3.5 x 10(3) class A sites (forming binary complexes with a half-life of 16.6 min) are present on A. tumefaciens genome, a large number of which show a distribution of 800-1000 base pairs. The rest have a more widely spaced distribution. The interactions between Escherichia coli RNA polymerase and the A. tumefaciens template have also been examined, and it has been observed that E. coli holoenzyme forms stable complexes with a shorter half-life and recognizes a lower number of class A sites on A. tumefaciens genome.

UI	MeSH Term	Description	Entries
D007700	Kinetics	The rate dynamics in chemical or physical systems.
D011485	Protein Binding	The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.	Plasma Protein Binding Capacity,Binding, Protein
D004259	DNA-Directed DNA Polymerase	DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.	DNA Polymerase,DNA Polymerases,DNA-Dependent DNA Polymerases,DNA Polymerase N3,DNA Dependent DNA Polymerases,DNA Directed DNA Polymerase,DNA Polymerase, DNA-Directed,DNA Polymerases, DNA-Dependent,Polymerase N3, DNA,Polymerase, DNA,Polymerase, DNA-Directed DNA,Polymerases, DNA,Polymerases, DNA-Dependent DNA
D004269	DNA, Bacterial	Deoxyribonucleic acid that makes up the genetic material of bacteria.	Bacterial DNA
D006493	Heparin	A highly acidic mucopolysaccharide formed of equal parts of sulfated D-glucosamine and D-glucuronic acid with sulfaminic bridges. The molecular weight ranges from six to twenty thousand. Heparin occurs in and is obtained from liver, lung, mast cells, etc., of vertebrates. Its function is unknown, but it is used to prevent blood clotting in vivo and vitro, in the form of many different salts.	Heparinic Acid,alpha-Heparin,Heparin Sodium,Liquaemin,Sodium Heparin,Unfractionated Heparin,Heparin, Sodium,Heparin, Unfractionated,alpha Heparin
D001482	Base Composition	The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.	Base Ratio,G+C Composition,Guanine + Cytosine Composition,G+C Content,GC Composition,GC Content,Guanine + Cytosine Content,Base Compositions,Base Ratios,Composition, Base,Composition, G+C,Composition, GC,Compositions, Base,Compositions, G+C,Compositions, GC,Content, G+C,Content, GC,Contents, G+C,Contents, GC,G+C Compositions,G+C Contents,GC Compositions,GC Contents,Ratio, Base,Ratios, Base
D001665	Binding Sites	The parts of a macromolecule that directly participate in its specific combination with another molecule.	Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D012231	Rhizobium	A genus of gram-negative, aerobic, rod-shaped bacteria that activate PLANT ROOT NODULATION in leguminous plants. Members of this genus are nitrogen-fixing and common soil inhabitants.
D012321	DNA-Directed RNA Polymerases	Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).	DNA-Dependent RNA Polymerases,RNA Polymerases,Transcriptases,DNA-Directed RNA Polymerase,RNA Polymerase,Transcriptase,DNA Dependent RNA Polymerases,DNA Directed RNA Polymerase,DNA Directed RNA Polymerases,Polymerase, DNA-Directed RNA,Polymerase, RNA,Polymerases, DNA-Dependent RNA,Polymerases, DNA-Directed RNA,Polymerases, RNA,RNA Polymerase, DNA-Directed,RNA Polymerases, DNA-Dependent,RNA Polymerases, DNA-Directed