7MLI image
Deposition Date 2021-04-28
Release Date 2022-02-02
Last Version Date 2023-10-18
Entry Detail
PDB ID:
7MLI
Keywords:
Title:
Crystal structure of Thermus thermophilus reiterative transcription complex with 5nt oligo-C RNA
Biological Source:
Method Details:
Experimental Method:
Resolution:
3.60 Å
R-Value Free:
0.29
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit alpha
Gene (Uniprot):rpoA
Chain IDs:A, B
Chain Length:315
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):rpoB
Chain IDs:C
Chain Length:1119
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta'
Gene (Uniprot):rpoC
Chain IDs:D
Chain Length:1524
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit omega
Gene (Uniprot):rpoZ
Chain IDs:E
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:RNA polymerase sigma factor SigA
Gene (Uniprot):sigA
Chain IDs:F
Chain Length:443
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*CP*TP*AP*CP*GP*GP*AP*TP*G)-3')
Chain IDs:H (auth: G)
Chain Length:20
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*CP*AP*TP*CP*CP*GP*TP*AP*GP*GP*GP*CP*GP*GP*G)-3')
Chain IDs:I (auth: H)
Chain Length:27
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*CP*CP*CP*CP*C)-3')
Chain IDs:G (auth: I)
Chain Length:5
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Structural and mechanistic basis of reiterative transcription initiation.
Proc.Natl.Acad.Sci.USA 119 ? ? (2022)
PMID: 35082149 DOI: 10.1073/pnas.2115746119

Abstact

Reiterative transcription initiation, observed at promoters that contain homopolymeric sequences at the transcription start site, generates RNA products having 5' sequences noncomplementary to the DNA template. Here, using crystallography and cryoelectron microscopy to define structures, protein-DNA photocrosslinking to map positions of RNAP leading and trailing edges relative to DNA, and single-molecule DNA nanomanipulation to assess RNA polymerase (RNAP)-dependent DNA unwinding, we show that RNA extension in reiterative transcription initiation 1) occurs without DNA scrunching; 2) involves a short, 2- to 3-bp, RNA-DNA hybrid; and 3) generates RNA that exits RNAP through the portal by which scrunched nontemplate-strand DNA exits RNAP in standard transcription initiation. The results establish that, whereas RNA extension in standard transcription initiation proceeds through a scrunching mechanism, RNA extension in reiterative transcription initiation proceeds through a slippage mechanism, with slipping of RNA relative to DNA within a short RNA-DNA hybrid, and with extrusion of RNA from RNAP through an alternative RNA exit.

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