3Q22

X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with GTP and Magnesium: substrate complex I

Summary for 3Q22

• Entry DOI: 10.2210/pdb3q22/pdb
• Related: 3Q0A 3Q23 3Q24
• Descriptor: Virion RNA polymerase, DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3'), GUANOSINE-5'-TRIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: protein-dna complex, two-metal catalysis, de novo transcription initiation, nucleotidyltransferase, initiation complex, dna-hairpin, virion rna polymerase, phosphate ion, transferase-dna complex, rna polymerase, transferase/dna
• Biological source: Enterobacteria phage N4 (Bacteriophage N4)
• Total number of polymer chains: 4
• Total formula weight: 270736.48

Authors

Gleghorn, M.L.,Murakami, K.S. (deposition date: 2010-12-19, release date: 2011-02-16, Last modification date: 2024-02-21)

Primary citation

Gleghorn, M.L.,Davydova, E.K.,Basu, R.,Rothman-Denes, L.B.,Murakami, K.S.
X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
Proc.Natl.Acad.Sci.USA, 108:3566-3571, 2011

PubMed Abstract: We have determined the X-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage N4 RNA polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit RNA polymerase. As observed during T7 RNA polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the O-helix, but only the correct base pairing between the +2 substrate and DNA base is able to complete the O-helix conformational transition. Substrate binding also facilitates catalytic metal binding that leads to alignment of the reactive groups of substrates for the nucleotidyl transfer reaction. Although all nucleic acid polymerases use two divalent metals for catalysis, they differ in the requirements and the timing of binding of each metal. In the case of bacteriophage RNA polymerase, we propose that catalytic metal binding is the last step before the nucleotidyl transfer reaction.

PubMed: 21321236
DOI: 10.1073/pnas.1016691108

Experimental method

X-RAY DIFFRACTION (2.11 Å)