8JKE image
Deposition Date 2023-06-01
Release Date 2024-02-14
Last Version Date 2024-04-03
Entry Detail
PDB ID:
8JKE
Title:
AfsR(T337A) transcription activation complex
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.67 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit alpha
Chain IDs:A, B, K
Chain Length:340
Number of Molecules:3
Biological Source:Streptomyces coelicolor A3(2)
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):rpoB
Chain IDs:C
Chain Length:1161
Number of Molecules:1
Biological Source:Streptomyces coelicolor A3(2)
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta'
Gene (Uniprot):rpoC
Chain IDs:D
Chain Length:1307
Number of Molecules:1
Biological Source:Streptomyces coelicolor A3(2)
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit omega
Gene (Uniprot):rpoZ
Chain IDs:E
Chain Length:90
Number of Molecules:1
Biological Source:Streptomyces coelicolor A3(2)
Polymer Type:polypeptide(L)
Molecule:RNA polymerase principal sigma factor HrdB
Gene (Uniprot):hrdB
Chain IDs:F
Chain Length:531
Number of Molecules:1
Biological Source:Streptomyces coelicolor A3(2)
Polymer Type:polypeptide(L)
Molecule:RNA polymerase-binding protein RbpA
Chain IDs:G
Chain Length:124
Number of Molecules:1
Biological Source:Streptomyces coelicolor A3(2)
Polymer Type:polypeptide(L)
Molecule:Putative transcriptional factor regulator
Gene (Uniprot):SCD8A.05
Chain IDs:H
Chain Length:160
Number of Molecules:1
Biological Source:Streptomyces coelicolor A3(2)
Polymer Type:polypeptide(L)
Molecule:Regulatory protein AfsR
Gene (Uniprot):afsR
Mutations:T337A
Chain IDs:I, J
Chain Length:1013
Number of Molecules:2
Biological Source:Streptomyces coelicolor A3(2)
Polymer Type:polydeoxyribonucleotide
Molecule:DNA(65-MER)
Chain IDs:L (auth: O)
Chain Length:65
Number of Molecules:1
Biological Source:Streptomyces coelicolor A3(2)
Polymer Type:polydeoxyribonucleotide
Molecule:DNA(65-MER)
Chain IDs:M (auth: P)
Chain Length:65
Number of Molecules:1
Biological Source:Streptomyces coelicolor A3(2)
Primary Citation
Structural and functional characterization of AfsR, an SARP family transcriptional activator of antibiotic biosynthesis in Streptomyces.
Plos Biol. 22 e3002528 e3002528 (2024)
PMID: 38427710 DOI: 10.1371/journal.pbio.3002528

Abstact

Streptomyces antibiotic regulatory proteins (SARPs) are widely distributed activators of antibiotic biosynthesis. Streptomyces coelicolor AfsR is an SARP regulator with an additional nucleotide-binding oligomerization domain (NOD) and a tetratricopeptide repeat (TPR) domain. Here, we present cryo-electron microscopy (cryo-EM) structures and in vitro assays to demonstrate how the SARP domain activates transcription and how it is modulated by NOD and TPR domains. The structures of transcription initiation complexes (TICs) show that the SARP domain forms a side-by-side dimer to simultaneously engage the afs box overlapping the -35 element and the σHrdB region 4 (R4), resembling a sigma adaptation mechanism. The SARP extensively interacts with the subunits of the RNA polymerase (RNAP) core enzyme including the β-flap tip helix (FTH), the β' zinc-binding domain (ZBD), and the highly flexible C-terminal domain of the α subunit (αCTD). Transcription assays of full-length AfsR and truncated proteins reveal the inhibitory effect of NOD and TPR on SARP transcription activation, which can be eliminated by ATP binding. In vitro phosphorylation hardly affects transcription activation of AfsR, but counteracts the disinhibition of ATP binding. Overall, our results present a detailed molecular view of how AfsR serves to activate transcription.

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