Database accession: MF7000614
Name: MarR family protein. OhrRC15S (apo form)
PDB ID: 1z91
Experimental method: X-ray (2.50 Å)
Assembly: Homodimer
Source organism: Bacillus subtilis
Primary publication of the structure:
Hong M, Fuangthong M, Helmann JD, Brennan RG
Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family.
(2005) Mol. Cell 20: 131-41
PMID: 16209951
Abstract:
The mechanisms by which Bacillus subtilis OhrR, a member of the MarR family of transcription regulators, binds the ohrA operator and is induced by oxidation of its lone cysteine residue by organic hydroperoxides to sulphenic acid are unknown. Here, we describe the crystal structures of reduced OhrR and an OhrR-ohrA operator complex. To bind DNA, OhrR employs a chimeric winged helix-turn-helix DNA binding motif, which is composed of extended eukaryotic-like wings, prokaryotic helix-turn-helix motifs, and helix-helix elements. The reactivity of the peroxide-sensing cysteine is not modulated by proximal basic residues but largely by the positive dipole of helix alpha1. Induction originates from the alleviation of intersubunit steric clash between the sulphenic acid moieties of the oxidized sensor cysteines and nearby tyrosines and methionines. The structure of the OhrR-ohrA operator complex reveals the DNA binding mechanism of the entire MarR family and suggests a common inducer binding pocket.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific
identical protein binding identical protein binding
protein homodimerization activity protein homodimerization activity
RNA polymerase II transcription regulatory region sequence-specific DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding
Biological process:
negative regulation of DNA-templated transcription negative regulation of DNA-templated transcription
negative regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II
regulation of DNA-templated transcription regulation of DNA-templated transcription
response to hydrogen peroxide response to hydrogen peroxide
response to stress response to stress
Cellular component:
cytoplasm cytoplasm
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Organic hydroperoxide resistance transcriptional regulator
Source organism: Bacillus subtilis
Length: 147 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMENKFDHMKLENQLCFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLHQKN
UniProtKB AC: O34777 (positions: 8-144)
Coverage: 93%
Name: Organic hydroperoxide resistance transcriptional regulator
Source organism: Bacillus subtilis
Length: 147 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMENKFDHMKLENQLCFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTILGLSKQSGEDLKQLKSALYTLLETLHQKN
UniProtKB AC: O34777 (positions: 8-144)
Coverage: 93%
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 A:
N/A
Chain A-2:
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)
Download this entry's XML file (.xml)
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