Database accession: MF7000718
Name: ArsR As(III)-responsive repressors
PDB ID: 6j0e
Experimental method: X-ray (1.60 Å)
Assembly: Homodimer
Source organism: Corynebacterium glutamicum
Primary publication of the structure:
Prabaharan C, Kandavelu P, Packianathan C, Rosen BP, Thiyagarajan S
Structures of two ArsR As(III)-responsive transcriptional repressors: Implications for the mechanism of derepression.
(2019) J. Struct. Biol. 207: 209-217
PMID: 31136796
Abstract:
ArsR As(III)-responsive transcriptional repressors, members of the ArsR/SmtB family of metalloregulatory proteins, have been characterized biochemically but, to date, no As(III)-bound structure has been solved. Here we report two crystal structures of ArsR repressors from Acidithiobacillus ferrooxidans (AfArsR) and Corynebacterium glutamicum (CgArsR) in the As(III)-bound form. AfArsR crystallized in P21 space group and diffracted up to 1.86 Å. CgArsR crystallized in P212121 and diffracted up to 1.6 Å. AfArsR showed one As(III) bound in one subunit of the homodimer, while the CgArsR structure showed two As(III) bound with S3 coordination, one in each monomer. Previous studies indicated that in AfArsR As(III) binds to Cys95, Cys96 and Cys102 from the same monomer, while, in CgArsR, to Cys15, Cys16 from one monomer and Cys55 from the other monomer. The dimer interfaces of these structures showed distinct differences from other members of the ArsR/SmtB family of proteins, which potentially renders multiple options for evolving metal(loid) binding sites in this family of proteins. Also, CgArsR presents a new α2-N binding site, not the previously predicted α3-N site. Despite differences in the location of the binding cysteines in the primary sequences of these proteins, the two metal binding sites are almost congruent on their structures, an example of convergent evolution. Analyses of the electrostatic surface of the proteins at the DNA binding domain indicate that there two different modes of derepression in the ArsR/SmtB family of metalloregulatory proteins.
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, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Arsenic responsive repressor ArsR
Source organism: Corynebacterium glutamicum
Length: 127 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTTLHTIQLANPTECCTLATGPLSSDESEHYADLFKVLGDPVRLRILSQLAAGGCGPVSVNELTDLMGLSQPTISHHLKKMTEAGFLDRVPEGRVVLHRVRPELFAELRTVLQIGSMELLEHHHHHH
UniProtKB AC: A0A5H1ZR36 (positions: 2-127)
Coverage: 99%
Name: Arsenic responsive repressor ArsR
Source organism: Corynebacterium glutamicum
Length: 127 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTTLHTIQLANPTECCTLATGPLSSDESEHYADLFKVLGDPVRLRILSQLAAGGCGPVSVNELTDLMGLSQPTISHHLKKMTEAGFLDRVPEGRVVLHRVRPELFAELRTVLQIGSMELLEHHHHHH
UniProtKB AC: A0A5H1ZR36 (positions: 3-127)
Coverage: 98%
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 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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