Database accession: MF7000706
Name: SMTB repressor (Synechococcus elongatus PCC 7942)
PDB ID: 1smt
Experimental method: X-ray (2.20 Å)
Assembly: Homodimer
Source organism: Synechococcus elongatus
Primary publication of the structure:
Cook WJ, Kar SR, Taylor KB, Hall LM
Crystal structure of the cyanobacterial metallothionein repressor SmtB: a model for metalloregulatory proteins.
(1998) J. Mol. Biol. 275: 337-46
PMID: 9466913
Abstract:
SmtB from Synechococcus PCC7942 is a trans-acting dimeric repressor that is required for Zn(2+)-responsive expression of the metallothionein SmtA. The structure of SmtB was solved using multiple isomorphous replacement techniques and refined at 2.2 A resolution by simulated annealing to an R-factor of 0.218. SmtB displays the classical helix-turn-helix motif found in many DNA-binding proteins. It has an alpha + beta topology, and the arrangement of the three core helices and the beta hairpin is similar to the HNF-3/fork head, CAP and diphtheria toxin repressor proteins. Although there is no zinc in the crystal structure, analysis of a mercuric acetate derivative suggests a total of four Zn2+ binding sites in the dimer. Two of these putative sites are at the opposite ends of the dimer, while the other two are at the dimer interface and are formed by residues contributed from each monomer. The structure of the dimer is such that simultaneous binding for both recognition helices to DNA would require either a bend in the DNA helix or a conformational change in the dimer. The structure of Synechococcus SmtB is the first in this family of metal-binding DNA repressors.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
DNA binding DNA binding
DNA-binding transcription factor activity DNA-binding transcription factor activity
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: Transcriptional repressor SmtB
Source organism: Synechococcus elongatus
Length: 122 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTKPVLQDGETVVCQGTHAAIASELQAIAPEVAQSLAEFFAVLADPNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVALYQNALDHLQECR
UniProtKB AC: P30340 (positions: 24-121)
Coverage: 80%
Name: Transcriptional repressor SmtB
Source organism: Synechococcus elongatus
Length: 122 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTKPVLQDGETVVCQGTHAAIASELQAIAPEVAQSLAEFFAVLADPNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVALYQNALDHLQECR
UniProtKB AC: P30340 (positions: 20-120)
Coverage: 82%
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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