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TitleStructural basis of Streptomyces transcription activation by zinc uptake regulator.
Journal, issue, pagesNucleic Acids Res, Vol. 50, Issue 14, Page 8363-8376, Year 2022
Publish dateAug 12, 2022
AuthorsXu Yang / Yiqun Wang / Guiyang Liu / Zixin Deng / Shuangjun Lin / Jianting Zheng /
PubMed AbstractStreptomyces coelicolor (Sc) is a model organism of actinobacteria to study morphological differentiation and production of bioactive metabolites. Sc zinc uptake regulator (Zur) affects both ...Streptomyces coelicolor (Sc) is a model organism of actinobacteria to study morphological differentiation and production of bioactive metabolites. Sc zinc uptake regulator (Zur) affects both processes by controlling zinc homeostasis. It activates transcription by binding to palindromic Zur-box sequences upstream of -35 elements. Here we deciphered the molecular mechanism by which ScZur interacts with promoter DNA and Sc RNA polymerase (RNAP) by cryo-EM structures and biochemical assays. The ScZur-DNA structures reveal a sequential and cooperative binding of three ScZur dimers surrounding a Zur-box spaced 8 nt upstream from a -35 element. The ScRNAPσHrdB-Zur-DNA structures define protein-protein and protein-DNA interactions involved in the principal housekeeping σHrdB-dependent transcription initiation from a noncanonical promoter with a -10 element lacking the critical adenine residue at position -11 and a TTGCCC -35 element deviating from the canonical TTGACA motif. ScZur interacts with the C-terminal domain of ScRNAP α subunit (αCTD) in a complex structure trapped in an active conformation. Key ScZur-αCTD interfacial residues accounting for ScZur-dependent transcription activation were confirmed by mutational studies. Together, our structural and biochemical results provide a comprehensive model for transcription activation of Zur family regulators.
External linksNucleic Acids Res / PubMed:35871291 / PubMed Central
MethodsEM (single particle)
Resolution3.4 - 10.8 Å
Structure data

EMDB-32048, PDB-7vo0:
Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (trimer of dimers)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-32049, PDB-7vo9:
Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (dimer of dimers)
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-32063, PDB-7vpd:
Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with one Zur dimers
Method: EM (single particle) / Resolution: 3.77 Å

EMDB-32077, PDB-7vpz:
Cryo-EM structure of Streptomyces coelicolor transcription initial complex with one Zur dimer
Method: EM (single particle) / Resolution: 4.14 Å

EMDB-33031: Cryo-EM structure of Streptomyces coelicolor transcription initial complex with two Zur dimers
PDB-7x74: Cryo-EM structure of Streptomyces coelicolor transcription initial complex with two Zur dimers.
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-33032, PDB-7x75:
Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with three Zur dimers
Method: EM (single particle) / Resolution: 3.45 Å

EMDB-33033, PDB-7x76:
Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with two Zur dimers
Method: EM (single particle) / Resolution: 3.67 Å

EMDB-33034: Focused map on the aCTD-Zur region of the Streptomyces coelicolor RNAP-promoter open complex with one Zur dimer
Method: EM (single particle) / Resolution: 10.5 Å

EMDB-33035: Focused map on the Zur region of the Streptomyces coelicolor RNAP-promoter open complex with two Zur dimers
Method: EM (single particle) / Resolution: 9.4 Å

EMDB-33036: Local refinement map of Zur regions in Streptomyces coelicolor RNAP-promoter open complex with three Zur dimers
Method: EM (single particle) / Resolution: 5.37 Å

EMDB-33037: Focused map on the Zur region of the Streptomyces coelicolor transcription initial complex with one Zur dimer
Method: EM (single particle) / Resolution: 10.8 Å

EMDB-33038: Focused map on the Zur region of the Streptomyces coelicolor transcription initial complex with two Zur dimers
Method: EM (single particle) / Resolution: 7.9 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • streptomyces coelicolor a3(2) (bacteria)
  • streptomyces coelicolor (strain atcc baa-471 / a3(2) / m145) (bacteria)
KeywordsDNA BINDING PROTEIN / GENE REGULATION / rna polymerase / zinc uptake regulator / Streptomyces / Open complex

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