Database accession: MF7000721
Name: C9S apo sulfide-responsive transcriptional repressor (SqrR) with diamide (Rhodobacter capsulatus)
PDB ID: 6o8m
Experimental method: X-ray (1.46 Å)
Assembly: Homodimer
Source organism: Rhodobacter capsulatus
Primary publication of the structure:
Capdevila DA, Walsh BJC, Zhang Y, Dietrich C, Gonzalez-Gutierrez G, Giedroc DP
Structural basis for persulfide-sensing specificity in a transcriptional regulator.
(2021) Nat. Chem. Biol. 17: 65-70
PMID: 33106663
Abstract:
Cysteine thiol-based transcriptional regulators orchestrate the coordinated regulation of redox homeostasis and other cellular processes by 'sensing' or detecting a specific redox-active molecule, which in turn activates the transcription of a specific detoxification pathway. The extent to which these sensors are truly specific in cells for a singular class of reactive small-molecule stressors, for example, reactive oxygen or sulfur species, is largely unknown. Here, we report structural and mechanistic insights into the thiol-based transcriptional repressor SqrR, which reacts exclusively with oxidized sulfur species such as persulfides, to yield a tetrasulfide bridge that inhibits DNA operator-promoter binding. Evaluation of crystallographic structures of SqrR in various derivatized states, coupled with the results of a mass spectrometry-based kinetic profiling strategy, suggest that persulfide selectivity is determined by structural frustration of the disulfide form. These findings led to the identification of an uncharacterized repressor from the bacterial pathogen Acinetobacter baumannii as a persulfide sensor.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
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: Transcriptional regulator, ArsR family
Source organism: Rhodobacter capsulatus
Length: 124 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMDTAQDPQDDFDPEMGSDTDERCAALDAEEMATRARAASNLLKALAHEGRLMIMCYLASGEKSVTELETRLSTRQAAVSQQLARLRLEGLVQSRREGKTIYYSLSDPRAARVVQTVYEQFCSGD
UniProtKB AC: D5AT91 (positions: 30-124)
Coverage: 76%
Name: Transcriptional regulator, ArsR family
Source organism: Rhodobacter capsulatus
Length: 124 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMDTAQDPQDDFDPEMGSDTDERCAALDAEEMATRARAASNLLKALAHEGRLMIMCYLASGEKSVTELETRLSTRQAAVSQQLARLRLEGLVQSRREGKTIYYSLSDPRAARVVQTVYEQFCSGD
UniProtKB AC: D5AT91 (positions: 30-124)
Coverage: 76%
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 (ArsR family) transcriptional regulator
Evidence level: Indirect evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
The N-terminal portion of the ArsR family transcriptional regulator, Mj223, is a helix-turn-helix (HTH) winged-helix DNA-binding motif. The C-terminal region of the protein is composed of two leucine-rich α-helices (H5 and H6) that form an antiparallel four-helix bundle with a large, hydrophobic interaction surface on dimerization that forms the hydrophobic core of the dimer (PMID:12471609, PMID:9466913). The C-terminal dimerization subdomain is a nice case of MSF. The protein is a dimer in solution (Dynamic light scattering) (PMID:12471609).
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)
Download this entry's JSON file (.json)
