7VO9

Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (dimer of dimers)

Summary for 7VO9

• Entry DOI: 10.2210/pdb7vo9/pdb
• EMDB information: 32049
• Descriptor: DNA (84-MER), Putative metal uptake regulation protein, ZINC ION, ... (4 entities in total)
• Functional Keywords: dna binding protein
• Biological source: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145); More
• Total number of polymer chains: 6
• Total formula weight: 120221.23

Authors

Yang, X.,Zheng, J. (deposition date: 2021-10-13, release date: 2022-08-03, Last modification date: 2024-06-19)

Primary citation

Yang, X.,Wang, Y.,Liu, G.,Deng, Z.,Lin, S.,Zheng, J.
Structural basis of Streptomyces transcription activation by zinc uptake regulator.
Nucleic Acids Res., 50:8363-8376, 2022

PubMed Abstract: 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.

PubMed: 35871291
DOI: 10.1093/nar/gkac627

Experimental method

ELECTRON MICROSCOPY (3.8 Å)