8JO2 | pdb_00008jo2

Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA

PDB DOI: https://doi.org/10.2210/pdb8JO2/pdb
EM Map EMD-36453: EMDB EMDataResource
NAKB: 8JO2

Classification: TRANSCRIPTION
Organism(s): synthetic construct, Escherichia coli BL21(DE3), Klebsiella pneumoniae JM45
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-06-06 Released: 2023-08-30
Deposition Author(s): Lou, Y.-C., Huang, H.-Y., Chen, C., Wu, K.-P.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan), Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA.

Lou, Y.C., Huang, H.Y., Yeh, H.H., Chiang, W.H., Chen, C., Wu, K.P.

(2023) Nucleic Acids Res 51: 10049-10058

PubMed: 37665001 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gkad724
Primary Citation Related Structures:
8JO2

PubMed Abstract:
PmrA, an OmpR/PhoB-family response regulator, triggers gene transcription responsible for polymyxin resistance in bacteria by recognizing promoters where the canonical-35 element is replaced by the pmra-box, representing the PmrA recognition sequence. Here, we report a cryo-electron microscopy (cryo-EM) structure of a bacterial PmrA-dependent transcription activation complex (TAC) containing a PmrA dimer, an RNA polymerase σ70 holoenzyme (RNAPH) and the pbgP promoter DNA. Our structure reveals that the RNAPH mainly contacts the PmrA C-terminal DNA-binding domain (DBD) via electrostatic interactions and reorients the DBD three base pairs upstream of the pmra-box, resulting in a dynamic TAC conformation. In vivo assays show that the substitution of the DNA-recognition residue eliminated its transcriptional activity, while variants with altered RNAPH-interacting residues resulted in enhanced transcriptional activity. Our findings suggest that both PmrA recognition-induced DNA distortion and PmrA promoter escape play crucial roles in its transcriptional activation.

Organizational Affiliation

Biomedical Translation Research Center, Academia Sinica, Taipei 11529, Taiwan.

Macromolecule Content

Total Structure Weight: 551 kDa
Atom Count: 35,368
Modeled Residue Count: 4,293
Deposited Residue Count: 4,693
Unique protein chains: 6
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	C [auth A], D [auth B]	329	Escherichia coli BL21(DE3)	Mutation(s): 0 Gene Names: rpoA, pez, phs, sez, b3295, JW3257 EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4 Go to UniProtKB: P0A7Z4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7Z4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	E [auth C]	1,342	Escherichia coli BL21(DE3)	Mutation(s): 0 Gene Names: rpoB EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12)) Explore P0A8V2 Go to UniProtKB: P0A8V2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8V2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	F [auth D]	1,407	Escherichia coli BL21(DE3)	Mutation(s): 0 Gene Names: rpoC EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12)) Explore P0A8T7 Go to UniProtKB: P0A8T7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8T7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	G [auth E]	91	Escherichia coli BL21(DE3)	Mutation(s): 0 Gene Names: rpoZ, b3649, JW3624 EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12)) Explore P0A800 Go to UniProtKB: P0A800
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A800
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor RpoD	H [auth F]	613	Escherichia coli BL21(DE3)	Mutation(s): 0 Gene Names: rpoD
UniProt
Find proteins for P00579 (Escherichia coli (strain K12)) Explore P00579 Go to UniProtKB: P00579
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00579
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding transcriptional regulator BasR	I [auth H], J [auth I]	226	Klebsiella pneumoniae JM45	Mutation(s): 0 Gene Names: N559_3529
UniProt
Find proteins for A0A0R4I965 (Klebsiella pneumoniae JM45) Explore A0A0R4I965 Go to UniProtKB: A0A0R4I965
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0R4I965
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (65-MER)	A [auth 1]	65	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (65-MER)	B [auth 2]	65	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	MOST 110-2311-B-001-046
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	MOST 108-2311-B-001-016-MY3
Academia Sinica (Taiwan)	Taiwan	AS-CDA-110-L03