Database accession: MF7000754
Name: Transcriptional regulator BldR (Sulfolobus solfataricus)
PDB ID: 3f3x
Experimental method: X-ray (1.90 Å)
Assembly: Homodimer
Source organism: Saccharolobus solfataricus
Primary publication of the structure:
Di Fiore A, Fiorentino G, Vitale RM, Ronca R, Amodeo P, Pedone C, Bartolucci S, De Simone G
Structural analysis of BldR from Sulfolobus solfataricus provides insights into the molecular basis of transcriptional activation in Archaea by MarR family proteins.
(2009) J. Mol. Biol. 388: 559-69
PMID: 19298823
Abstract:
The multiple antibiotic resistance regulator (MarR) family constitutes a significant class of transcriptional regulators whose members control a variety of important biological functions such as regulation of response to environmental stress, control of virulence factor production, resistance to antimicrobial agents, and regulation of aromatic catabolic pathways. Although the majority of MarR family members have been characterized as transcriptional repressors, a few examples of transcriptional activators have also been reported. BldR is a newly identified member of this family that has been demonstrated to act as a transcriptional activator in stress response to aromatic compounds in the crenarchaeon Sulfolobus solfataricus. In this work, we report findings on the BldR X-ray crystal structure and present a molecular modeling study on the complex that this protein forms with its cognate DNA sequence, thus providing the first detailed description of the DNA-binding mechanism of an archaeal activator belonging to the MarR family. Two residues responsible for the high binding specificity of this transcriptional regulator were also identified. Our studies demonstrated that, in Archaea, the capability of MarR family members to act as activators or repressors is not related to a particular DNA-binding mechanism but rather could be due to the position of the binding site on the target DNA. Moreover, since genes encoding MarR proteins often control transcription of operons that encode for multisubstrate efflux pumps, our results also provided important insights for the identification of new tools to overcome the microorganism's multidrug resistance.
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: 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: Transcriptional regulator, marR family, putative
Source organism: Saccharolobus solfataricus
Length: 144 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMQKIDEKLQLMNTIAKIYRGSIKEFNNRLGKLMNLSYLDFSILKATSEEPRSMVYLANRYFVTQSAITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVLLEANEVLRNLVNEMLSDVENVEELLEGLNKILSRIGSSKD
UniProtKB AC: Q97YG9 (positions: 1-140)
Coverage: 97%
Name: Transcriptional regulator, marR family, putative
Source organism: Saccharolobus solfataricus
Length: 144 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMQKIDEKLQLMNTIAKIYRGSIKEFNNRLGKLMNLSYLDFSILKATSEEPRSMVYLANRYFVTQSAITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVLLEANEVLRNLVNEMLSDVENVEELLEGLNKILSRIGSSKD
UniProtKB AC: Q97YG9 (positions: 1-140)
Coverage: 97%
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 II) transcriptional regulator
Evidence level: Indirect evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
Thermal unfolding measured with circular dichroism of the MarR family protein, HucR, suggested two-state model of unfolding (PMID:15448166). Also, a decrease in pH induced a molten globule-like state, where the protein remained in dimeric form (PMID:27282811). Helices 1, 2, 6 and 7 form the dimerization subdomain, they form an apparently stable dimer interface that preconfigures the DNA recognition HTH subdomain for DNA binding (PMID:16750221).
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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