Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of Streptomyces transcription activation by zinc uptake regulator.
Journal, issue, pages	Nucleic Acids Res, Vol. 50, Issue 14, Page 8363-8376, Year 2022
Publish date	Aug 12, 2022
Authors	Xu Yang / Yiqun Wang / Guiyang Liu / Zixin Deng / Shuangjun Lin / Jianting Zheng /
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 ...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 links	Nucleic Acids Res / PubMed:35871291 / PubMed Central
Methods	EM (single particle)
Resolution	3.4 - 10.8 Å
Structure data	32048 7vo0 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 32049 7vo9 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 32063 7vpd 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 32077 7vpz 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 33031 7x74 EMDB-33031, PDB-7x74: Cryo-EM structure of Streptomyces coelicolor transcription initial complex with two Zur dimers. Method: EM (single particle) / Resolution: 3.7 Å 33032 7x75 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 33033 7x76 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)
Keywords	DNA BINDING PROTEIN / GENE REGULATION / rna polymerase / zinc uptake regulator / Streptomyces / Open complex