Loading
PDBj
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

3Q24

X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with pppGpG and pyrophosphate: product complex

Summary for 3Q24
Entry DOI10.2210/pdb3q24/pdb
Related3Q0A 3Q22 3Q23
DescriptorVirion 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, ... (7 entities in total)
Functional Keywordsprotein-dna complex, two-metal catalysis, de novo transcription initiation, nucleotidyltransferase, initiation complex, dna-hairpin, virion rna polymerase, transferase-dna-rna complex, transferase/dna/rna
Biological sourceEnterobacteria phage N4 (Bacteriophage N4)
More
Total number of polymer chains4
Total formula weight269519.10
Authors
Gleghorn, M.L.,Murakami, K.S. (deposition date: 2010-12-19, release date: 2011-02-16, Last modification date: 2024-10-16)
Primary citationGleghorn, 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
Cited by
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
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.81 Å)
Structure validation

227561

PDB entries from 2024-11-20

PDB statisticsPDBj update infoContact PDBjnumon