Database accession: MF7000665
Name: RosR (vng0258) grown from NaBr (Halobacterium salinarum)
PDB ID: 6ez1
Experimental method: X-ray (1.75 Å)
Assembly: Homodimer
Source organism: Halobacterium salinarum
Primary publication of the structure:
Kutnowski N, Shmuely H, Dahan I, Shmulevich F, Davidov G, Shahar A, Eichler J, Zarivach R, Shaanan B
The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.
(2018) J. Struct. Biol. 204: 191-198
PMID: 30110657
Abstract:
Protein-DNA interactions are highly dependent on salt concentration. To gain insight into how such interactions are maintained in the highly saline cytoplasm of halophilic archaea, we determined the 3-D structure of VNG0258H/RosR, the first haloarchaeal DNA-binding protein from the extreme halophilic archaeon Halobactrium salinarum. It is a dimeric winged-helix-turn-helix (wHTH) protein with unique features due to adaptation to the halophilic environment. As ions are major players in DNA binding processes, particularly in halophilic environments, we investigated the solution structure of the ionic envelope and located anions in the first shell around the protein in the crystal using anomalous scattering. Anions that were found to be tightly bound to residues in the positively charged DNA-binding site would probably be released upon DNA binding and will thus make significant contribution to the driving force of the binding process. Unexpectedly, ions were also found in a buried internal cavity connected to the external medium by a tunnel. Our structure lays a solid groundwork for future structural, computational and biochemical studies on complexes of the protein with cognate DNA sequences, with implications to protein-DNA interactions in hyper-saline environments.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
metal ion binding metal ion binding
Biological process: not assigned
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: PadR family transcription regulator RosR
Source organism: Halobacterium salinarum
Length: 116 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSEAQPDARSDARDLTAFQKNILTVLGEEARYGLAIKRELEEYYGEEVNHGRLYPNLDDLVNKGLVEKSELDKRTNEYALTNEGFDAVVDDLEWTLSKFVADADRRERVETIVADD
UniProtKB AC: Q9HSF4 (positions: 11-116)
Coverage: 91%
Name: PadR family transcription regulator RosR
Source organism: Halobacterium salinarum
Length: 116 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSEAQPDARSDARDLTAFQKNILTVLGEEARYGLAIKRELEEYYGEEVNHGRLYPNLDDLVNKGLVEKSELDKRTNEYALTNEGFDAVVDDLEWTLSKFVADADRRERVETIVADD
UniProtKB AC: Q9HSF4 (positions: 11-116)
Coverage: 91%
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 (PadR family) transcriptional regulator
Evidence level: Direct evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
AphA monomers were found to be highly unstable (PMID:15647287). AphA is a dimer with an N-terminal winged helix DNA-binding domain and a unique C-terminal antiparallel coiled coil domain that serves as its primary dimerization interface and is a case of mutual synergistic folding (MSF). Another PadR family transcriptional regulator, Rv3488, was shown to be a dimer in solution (PMID:30266832), while differential scanning calorimetry-based thermal denaturation data suggested that the PadR family Rv1176c follows two-state unfolding (PMID:38417748).
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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