Database accession: MF7000255
Name: MarR (Clostridioides difficile)
PDB ID: 5eri
Experimental method: X-ray (2.30 Å)
Assembly: Homodimer
Source organism: Clostridioides difficile
Primary publication of the structure:
Peng JW, Yuan H, Tan XS
Crystal structure of the multiple antibiotic resistance regulator MarR from Clostridium difficile.
(2017) Acta Crystallogr F Struct Biol Commun 73: 363-368
PMID: 28580925
Abstract:
Regulators of multiple antibiotic resistance (MarRs) are key players against toxins in prokaryotes. MarR homologues have been identified in many bacterial and archaeal species which pose daunting antibiotic resistance issues that threaten public health. The continuous prevalence of Clostridium difficile infection (CDI) throughout the world is associated with the abuse of antibiotics, and antibiotic treatments of CDI have limited effect. In the genome of C. difficile strain 630, the marR gene (ID 4913953) encodes a MarR protein. Here, MarR from C. difficile (MarRC.difficile) was subcloned and crystallized for the first time. MarRC.difficile was successfully expressed in Escherichia coli in a soluble form and was purified to near-homogeneity (>95%) by a two-step purification protocol. The structure of MarRC.difficile has been solved at 2.3 Å resolution. The crystal belonged to the monoclinic space group P43212, with unit-cell parameters a = b = 66.569, c = 83.654 Å. The structure reported reveals MarRC.difficile to be a dimer, with each subunit consisting of six α-helices and three antiparallel β-hairpins. MarRC.difficile shows high structural similarity to the MarR proteins from E. coli and Staphylococcus aureus, indicating that MarRC.difficile might be a DNA-binding protein.
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: not assigned
Cellular component: not assigned
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: DNA-binding transcriptional repressor MarR
Source organism: Clostridioides difficile
Length: 149 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMIKTLDSNILREVGTLSRAVNSINDIKYKELKLQKGQFTFLTRICENPGINLVELSNMLKVDKATTTKAIQKLIKAGYVDKKQDKFDKRGYNLTPTDKSLEVYELIIEEENRSIEICFDNFTDEEKQVVTKLLEKMSKNVENEWFKVKR
UniProtKB AC: A0A031WDA8 (positions: 2-148)
Coverage: 98%
Name: DNA-binding transcriptional repressor MarR
Source organism: Clostridioides difficile
Length: 149 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMIKTLDSNILREVGTLSRAVNSINDIKYKELKLQKGQFTFLTRICENPGINLVELSNMLKVDKATTTKAIQKLIKAGYVDKKQDKFDKRGYNLTPTDKSLEVYELIIEEENRSIEICFDNFTDEEKQVVTKLLEKMSKNVENEWFKVKR
UniProtKB AC: A0A031WDA8 (positions: 2-148)
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 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)
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