8cwt | pdb_00008cwt
Complex structure of WhiB3 and the SigmaAr4-RNAP Beta flap tip chimera in space group P43212
Structural highlights
FunctionWHIB3_MYCTU A redox-sensitive transcriptional regulator. Maintains intracellular redox homeostasis by regulating catabolic metabolism and polyketide biosynthesis (PubMed:17609386, PubMed:19680450). Regulates expression of the redox buffer ergothioneine (ERG) in a carbon-source-dependent manner; loss of ERG or mycothiol (MSH, the other major redox buffer in this bacteria) leads to respiratory alterations and bioenergetic deficiencies that negatively impact virulence (PubMed:26774486). In response to low external pH (like that found in host macrophage phagosomes) alters endogenous gene expression leading to acid resistance; MSH and WhiB3 are probably part of a regulatory circuit that mediates gene expression upon acid stress (PubMed:26637353). Regulates pathogenic lipid synthesis, coordinating proprionate flux (and other host-derived fatty acid oxidation intermediates) into methyl-branched fatty acids (polyacyltrehalose, phthiocerol dimycocerosates, sulfolipids) and the storage lipid triacylglycerol, functioning as reductive sink (PubMed:19680450). During intracellular growth M.tuberculosis uses host fatty acids as an energy source, generating large quantities of proprionate and NADH/NADPH, which are toxic and highly reducing respectively. WhiB3 is thought to help dissipate proprionate and NADH/NADPH by switching to the in vivo carbon source and via lipid anabolism (PubMed:19680450). Responds to NO and O(2) (PubMed:17609386). Regulates expression of genes encoding modular polyketide synthases such as pks2, pks3 and fbpA (PubMed:19680450). The oxidized apo-form of WhiB3 binds DNA (with 2 intramolecular disulfide bonds); holo-WhiB3 (with the 4Fe-4S cluster) binds DNA considerably less well (PubMed:19680450). Discriminates poorly between specific and non-specific DNA-binding. Plays a role in virulence and nutritional stress (PubMed:11880648, PubMed:17609386, PubMed:26637353). In its apo-form can act as a protein disulfide reductase (PubMed:18550384).[1] [2] [3] [4] [5] [6] [7] May respond to mycothiol (MSH) redox potential (E-MSH) which decreases at pH 4.5 for up to 72 hours, indicative of cellular reductive stress; deletion of whiB3 leads to a lesser E-MSH at 72 hours, indicative of cellular oxidative stress (PubMed:26637353). Probably via its effects on production of polyketide lipids, regulates host gene expression, leading to blockage of phagosome maturation (PubMed:26637353). Equilibration of extra- and intracytoplasmic pH kills bacteria (PubMed:26637353).[8] Publication Abstract from PubMedMycobacterium tuberculosis (Mtb) WhiB3 is an iron-sulfur cluster-containing transcription factor belonging to a subclass of the WhiB-Like (Wbl) family that is widely distributed in the phylum Actinobacteria. WhiB3 plays a crucial role in the survival and pathogenesis of Mtb. It binds to the conserved region 4 of the principal sigma factor (sigma(A)(4)) in the RNA polymerase holoenzyme to regulate gene expression like other known Wbl proteins in Mtb. However, the structural basis of how WhiB3 coordinates with sigma(A)(4) to bind DNA and regulate transcription is unclear. Here we determined crystal structures of the WhiB3:sigma(A)(4) complex without and with DNA at 1.5 A and 2.45 A, respectively, to elucidate how WhiB3 interacts with DNA to regulate gene expression. These structures reveal that the WhiB3:sigma(A)(4) complex shares a molecular interface similar to other structurally characterized Wbl proteins and also possesses a subclass-specific Arg-rich DNA binding motif. We demonstrate that this newly defined Arg-rich motif is required for WhiB3 binding to DNA in vitro and transcriptional regulation in Mycobacterium smegmatis (Msm). Together, our study provides empirical evidence of how WhiB3 regulates gene expression in Mtb by partnering with sigma(A)(4) and engaging with DNA via the subclass-specific structural motif, distinct from the modes of DNA interaction by WhiB1 and WhiB7. Structural Basis of DNA Binding by the WhiB-Like Transcription Factor WhiB3 in Mycobacterium tuberculosis.,Wan T, Horova M, Khetrapal V, Li S, Jones C, Schacht A, Sun X, Zhang L J Biol Chem. 2023 May 2:104777. doi: 10.1016/j.jbc.2023.104777. PMID:37142222[9] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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