title: Swing-gate model of nucleotide entry into the RNA polymerase active center.
abstract: Each elementary step of transcription involves translocation of the 3' terminus of RNA in the RNA polymerase active center, followed by the entry of a nucleoside triphosphate. The structural basis of these transitions was studied using RNA-protein crosslinks. The contacts were mapped and projected onto the crystal structure, in which the "F bridge" helix in the beta' subunit is either bent or relaxed. Bending/relaxation of the F bridge correlates with lateral movements of the RNA 3' terminus. The bent conformation is sterically incompatable with the occupancy of the nucleotide site, suggesting that the switch regulates both the entry of substrates and the translocation of the transcript. The switch occurs as part of a cooperative transition of a larger structural domain that consists of the F helix and the supporting G loop.
authors.affiliation: Public Health Research Institute, Newark, NJ 07103, USA.
authors.forename: Vitaliy
authors.initials: V
authors.lastname: Epshtein
authors.forename: Arkady
authors.initials: A
authors.lastname: Mustaev
authors.forename: Vadim
authors.initials: V
authors.lastname: Markovtsov
authors.forename: Oxana
authors.initials: O
authors.lastname: Bereshchenko
authors.forename: Vadim
authors.initials: V
authors.lastname: Nikiforov
authors.forename: Alex
authors.initials: A
authors.lastname: Goldfarb
mesh_terms: D001665:Binding Sites; D003432:Cross-Linking Reagents / Q000378:metabolism; D018360:Crystallography, X-Ray; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D046911:Macromolecular Substances; D008958:Models, Molecular; D015394:Molecular Structure; D009711:Nucleotides / Q000378:metabolism*; D017354:Point Mutation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D021122:Protein Subunits; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D003432:Cross-Linking Reagents; D046911:Macromolecular Substances; D009711:Nucleotides; D021122:Protein Subunits; D012321:DNA-Directed RNA Polymerases