Database accession: MF7000751
Name: HucR (Deinococcus radiodurans)
PDB ID: 2fbk
Experimental method: X-ray (2.30 Å)
Assembly: Homodimer
Source organism: Deinococcus radiodurans
Primary publication of the structure:
Bordelon T, Wilkinson SP, Grove A, Newcomer ME
The crystal structure of the transcriptional regulator HucR from Deinococcus radiodurans reveals a repressor preconfigured for DNA binding.
(2006) J. Mol. Biol. 360: 168-77
PMID: 16750221
Abstract:
We report here the 2.3 A resolution structure of the hypothetical uricase regulator (HucR) from Deinococcus radiodurans R1. HucR, a member of the MarR family of DNA-binding proteins, was previously shown to repress its own expression as well as that of a uricase, a repression that is alleviated both in vivo and in vitro upon binding uric acid, the substrate for uricase. As uric acid is a potent scavenger of reactive oxygen species, and as D. radiodurans is known for its remarkable resistance to DNA-damaging agents, these observations indicate a novel oxidative stress response mechanism. The crystal structure of HucR in the absence of ligand or DNA reveals a dimer in which the DNA recognition helices are preconfigured for DNA binding. This configuration of DNA-binding domains is achieved through an apparently stable dimer interface that, in contrast to what is observed in other MarR homologs for which structures have been determined, shows little conformational heterogeneity in the absence of ligand. An additional amino-terminal segment, absent from other MarR homologs, appears to brace the principal helix of the dimerization interface. However, although HucR is preconfigured for DNA binding, the presence of a stacked pair of symmetry-related histidine residues at a central pivot point in the dimer interface suggests a mechanism for a conformational change to attenuate DNA binding.
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:
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, B
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
Source organism: Deinococcus radiodurans
Length: 181 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSARMDNDTAALLERIRSDWARLNHGQGPDSDGLTPSAGPMLTLLLLERLHAALGREIERTYAASGLNAAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTHLLPAHLATTQRVLAPLSAQEQRTLEELAGRMLAGLEQGV
UniProtKB AC: Q9RV71 (positions: 8-179)
Coverage: 95%
Name: Transcriptional regulator, MarR family
Source organism: Deinococcus radiodurans
Length: 181 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSARMDNDTAALLERIRSDWARLNHGQGPDSDGLTPSAGPMLTLLLLERLHAALGREIERTYAASGLNAAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTHLLPAHLATTQRVLAPLSAQEQRTLEELAGRMLAGLEQGV
UniProtKB AC: Q9RV71 (positions: 8-179)
Coverage: 95%
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 B:
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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