8E79 | pdb_00008e79

Classification: TRANSCRIPTION/DNA/RNA
Organism(s): Mycobacterium tuberculosis, Escherichia coli, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-08-23 Released: 2023-03-22
Deposition Author(s): Delbeau, M., Darst, S.A., Campbell, E.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

(2023) Mol Cell 83: 1474-1488.e8

PubMed Abstract:
Transcriptional pauses mediate regulation of RNA biogenesis. DNA-encoded pause signals trigger pausing by stabilizing RNA polymerase (RNAP) swiveling and inhibiting DNA translocation. The N-terminal domain (NGN) of the only universal transcription factor, NusG/Spt5, modulates pausing through contacts to RNAP and DNA. Pro-pausing NusGs enhance pauses, whereas anti-pausing NusGs suppress pauses. Little is known about pausing and NusG in the human pathogen Mycobacterium tuberculosis (Mtb). We report that MtbNusG is pro-pausing. MtbNusG captures paused, swiveled RNAP by contacts to the RNAP protrusion and nontemplate-DNA wedged between the NGN and RNAP gate loop. In contrast, anti-pausing Escherichia coli (Eco) NGN contacts the MtbRNAP gate loop, inhibiting swiveling and pausing. Using CRISPR-mediated genetics, we show that pro-pausing NGN is required for mycobacterial fitness. Our results define an essential function of mycobacterial NusG and the structural basis of pro- versus anti-pausing NusG activity, with broad implications for the function of all NusG orthologs.

Organizational Affiliation

Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	347	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: rpoA EC: 2.7.7.6
UniProt
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGZ1 Go to UniProtKB: P9WGZ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGZ1
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C	1,172	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: rpoB, MRA_0676 EC: 2.7.7.6
UniProt
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY9 Go to UniProtKB: P9WGY9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGY9
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	1,318	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: rpoC, E5M52_05480, ERS007665_00591, ERS013471_00574, ERS023446_00410, ERS075361_00813, ERS094182_01340, F6W99_03342 EC: 2.7.7.6
UniProt
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY7 Go to UniProtKB: P9WGY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGY7
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E	110	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: rpoZ, ERS007703_04032, ERS007720_04749, ERS094182_01030 EC: 2.7.7.6
UniProt
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY5 Go to UniProtKB: P9WGY5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGY5
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription termination/antitermination protein NusG	F [auth N]	181	Escherichia coli	Mutation(s): 0 Gene Names: nusG
UniProt
Find proteins for P0AFG0 (Escherichia coli (strain K12)) Explore P0AFG0 Go to UniProtKB: P0AFG0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFG0
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
DNA (54-MER)	G [auth O]	54	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
DNA (54-MER)	H [auth P]	54	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 8
RNA (42-MER)	I [auth R]	42	synthetic construct
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Reference Sequence

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D]	J [auth D], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain J [auth D] Focus chain K [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]