Database accession: MF7000623
Name: Transcriptional regulator (Bacillus subtilis, strain 168)
PDB ID: 7wze
Experimental method: X-ray (2.65 Å)
Assembly: Homodimer
Source organism: Bacillus subtilis
Primary publication of the structure:
Park J, Kim J, Choi Z, Hong M
Structure-based molecular characterization of the YetL transcription factor from Bacillus subtilis.
(2022) Biochem. Biophys. Res. Commun. 607: 146-151
PMID: 35367827
Abstract:
Bacillus subtilis is a gram-positive bacterium that has developed to coordinate gene expression and to survive against changes of nutrients and toxic chemicals. Flavonoids are exuded by plant cells and are abundant in the soil. To counteract the antibacterial effects of flavonoids, B. subtilis expresses flavonoid-detoxifying enzymes, and their expression is negatively regulated by transcription factors, including YetL. YetL was shown to control B. subtilis growth through the promoter regions of yetL and yetM genes in response to some flavonoids. Despite the functional significance of the YetL transcription factor in bacterial survival, no structural information is available for YetL. Here, we report the crystal structure of YetL and propose a flavonoid-induced regulatory mechanism. The YetL structure contains the canonical winged helix-turn-helix motif of the MarR superfamily but distinctly presents an additional N-terminal helix. In the dimeric assembly of YetL, the H1 helix intersects the YetL dimer and contributes to extensive intersubunit interactions. As a transcription factor, YetL recognizes a 28-mer operator of double-stranded DNA that contains a palindromic sequence. Moreover, our comparative structural analysis of YetL and other MarR members allows us to propose a flavonoid-induced transcription regulatory mechanism that is used for bacterial adaptation to environmental changes and stresses.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
DNA binding DNA binding
DNA-binding transcription factor activity DNA-binding transcription factor activity
Biological process:
regulation of DNA-templated transcription regulation of DNA-templated transcription
response to stress response to stress
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: Y, A
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: HTH-type transcriptional repressor YetL
Source organism: Bacillus subtilis
Length: 167 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMELKHLPKYKHITEHAETYANIDAGSLELFLSLFDISKKMNHVMEHYFAGRGLSEGKFKILMLLFDAKDHRLSPTELAKRSNVTKATITGLLDGLARDGFVSRRHHTEDKRKISIELTTEGKARLEQFLPGHFSKISAVMENYSDEEKDMFVKMLGDLFERLSVFKD
UniProtKB AC: O31541 (positions: 2-167)
Coverage: 99%
Name: HTH-type transcriptional repressor YetL
Source organism: Bacillus subtilis
Length: 167 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMELKHLPKYKHITEHAETYANIDAGSLELFLSLFDISKKMNHVMEHYFAGRGLSEGKFKILMLLFDAKDHRLSPTELAKRSNVTKATITGLLDGLARDGFVSRRHHTEDKRKISIELTTEGKARLEQFLPGHFSKISAVMENYSDEEKDMFVKMLGDLFERLSVFKD
UniProtKB AC: O31541 (positions: 2-166)
Coverage: 98%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Winged helix DNA-binding domain (MarR type I) transcriptional regulator
Evidence level: Direct evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
The MarR-type family transcriptional regulator, NadR is dimeric in solution (SE-HPLC/MALLS) as other MarR faimily proteins (PMID:18272181). Compared to ligand-stabilized holo-NadR, apo-NadR displayed an intrinsic flexibility focused in the DNA-binding region (PMID:27105075). The structural features of several family members have been described, they all have two subdomains: there is a helix-turn-helix (HTH) DNA-binding domain plus dimerization helices that form an interlocked dimerization domain. Dimerization is mediated by helices α1, α5, and α6 from each monomer resulting in an interlocked, tight dimer burying a large, hydrophobic solvent-accessible surface area. The structure of the dimerization region reveals domain swapping, where α1 of one subunit is inserted between α5′ and α6′ of the other subunit and forms a coiled coil with helix α6′ (PMID:19586910). The DNA-binding elements contain helices α3-α4 and strands β1-β2 from each monomer (PMID:29794028, PMID:35367827).
Chain Y:
N/A
Chain A:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
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