Database accession: MF7000759
Name: HucR with urate
PDB ID: 7xl9
Experimental method: X-ray (2.58 Å)
Assembly: Homodimer
Source organism: Deinococcus radiodurans
Primary publication of the structure:
Rho S, Jung W, Park JK, Choi MH, Kim M, Kim J, Byun J, Park T, Lee BI, Wilkinson SP, Park S
The structure of Deinococcus radiodurans transcriptional regulator HucR retold with the urate bound.
(2022) Biochem. Biophys. Res. Commun. 615: 63-69
PMID: 35605407
Abstract:
HucR is a MarR family protein of Deinococcus radiodurans, which binds tightly to the intergenic region of HucR and the uricase gene to inhibit their expression. Urate (or uric acid) antagonizes the repressor function of HucR by binding to HucR to impede its association with the cognate DNA. The previously reported crystal structure of HucR was without the bound urate showing significant structural homology to other MarR structures. In this paper, we report the crystal structure of HucR determined with the urate bound. However, despite the fact that the urate is found at a site well-known to harbor ligands in other MarR family proteins, the overall HucR structure indicates that no significant change in structure takes place with the urate bound. Structure analysis further suggests that the urate interaction in HucR is mediated by histidine/glutamate side chains and ordered water molecules stabilized by various residues. Such interaction is quite unique compared to other known structural interactions between urate and its binding proteins. Furthermore, structural comparison of the apo- and the urate bound forms allows us to hypothesize that the Trp20-mediated water network in the apo-form stabilizes the proper HucR fold for cognate DNA binding, and that urate binding, also via Trp20, and the consequent reorganization of water molecules in the binding pocket, likely disrupts the DNA binding configuration to result in the attenuated 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, 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
Source organism: Deinococcus radiodurans
Length: 181 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSARMDNDTAALLERIRSDWARLNHGQGPDSDGLTPSAGPMLTLLLLERLHAALGREIERTYAASGLNAAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTHLLPAHLATTQRVLAPLSAQEQRTLEELAGRMLAGLEQGV
UniProtKB AC: Q9RV71 (positions: 8-181)
Coverage: 96%
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: 8-181)
Coverage: 96%
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)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
