title: Elongation complexes of Thermus thermophilus RNA polymerase that possess distinct translocation conformations.
abstract: We have characterized elongation complexes (ECs) of RNA polymerase from the extremely thermophilic bacterium, Thermus thermophilus. We found that complexes assembled on nucleic acid scaffolds are transcriptionally competent at high temperature (50-80 degrees C) and, depending upon the organization of the scaffold, possess distinct translocation conformations. ECs assembled on scaffolds with a 9 bp RNA:DNA hybrid are highly stable, resistant to pyrophosphorolysis, and are in the posttranslocated state. ECs with an RNA:DNA hybrid longer or shorter than 9 bp appear to be in a pretranslocated state, as evidenced by their sensitivity to pyrophosphorolysis, GreA-induced cleavage, and exonuclease footprinting. Both pretranslocated (8 bp RNA:DNA hybrid) and posttranslocated (9 bp RNA:DNA hybrid) complexes were crystallized in distinct crystal forms, supporting the homogeneity of the conformational states in these complexes. Crystals of a posttranslocated complex were used to collect diffraction data at atomic resolution.
authors.affiliation: Department of Cell Biology, University of Medicine and Dentistry of New Jersey, School of Osteopathic Medicine, Stratford, NJ 08084, USA.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Kashkina
authors.forename: Michael
authors.initials: M
authors.lastname: Anikin
authors.forename: Tahir H
authors.initials: TH
authors.lastname: Tahirov
authors.forename: Sergei N
authors.initials: SN
authors.lastname: Kochetkov
authors.forename: Dmitry G
authors.initials: DG
authors.lastname: Vassylyev
authors.forename: Dmitry
authors.initials: D
authors.lastname: Temiakov
mesh_terms: D003460:Crystallization; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000378:metabolism*; D004720:Endonucleases / Q000378:metabolism; D005092:Exonucleases / Q000378:metabolism; D009696:Nucleic Acids / Q000737:chemistry; D011487:Protein Conformation; D021381:Protein Transport; D016963:Thermus thermophilus / Q000201:enzymology*; D014158:Transcription, Genetic
chemical_list: D009696:Nucleic Acids; D012321:DNA-Directed RNA Polymerases; D004720:Endonucleases; D005092:Exonucleases