Database accession: MF7000658
Name: Circadian clock modifier, Pex (Cyanobacterium)
PDB ID: 2e1n
Experimental method: X-ray (1.80 Å)
Assembly: Homodimer
Source organism: Synechococcus elongatus
Primary publication of the structure:
Arita K, Hashimoto H, Igari K, Akaboshi M, Kutsuna S, Sato M, Shimizu T
Structural and biochemical characterization of a cyanobacterium circadian clock-modifier protein.
(2007) J. Biol. Chem. 282: 1128-35
PMID: 17098741
Abstract:
Circadian clocks are self-sustained biochemical oscillators. The oscillator of cyanobacteria comprises the products of three kai genes (kaiA, kaiB, and kaiC). The autophosphorylation cycle of KaiC oscillates robustly in the cell with a 24-h period and is essential for the basic timing of the cyanobacterial circadian clock. Recently, period extender (pex), mutants of which show a short period phenotype, was classified as a resetting-related gene. In fact, pex mRNA and the pex protein (Pex) increase during the dark period, and a pex mutant subjected to diurnal light-dark cycles shows a 3-h advance in rhythm phase. Here, we report the x-ray crystallographic analysis and biochemical characterization of Pex from cyanobacterium Synechococcus elongatus PCC 7942. The molecule has an (alpha+beta) structure with a winged-helix motif and is indicated to function as a dimer. The subunit arrangement in the dimer is unique and has not been seen in other winged-helix proteins. Electrophoresis mobility shift assay using a 25-base pair complementary oligonucleotide incorporating the kaiA upstream sequence demonstrates that Pex has an affinity for the double-stranded DNA. Furthermore, mutation analysis shows that Pex uses the wing region to recognize the DNA. The in vivo rhythm assay of Pex shows that the constitutive expression of the pex gene harboring the mutation that fails to bind to DNA lacks the period-prolongation activity in the pex-deficient Synechococcus, suggesting that Pex is a DNA-binding transcription factor.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.Molecular function: not assigned
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 regulator, PadR family
Source organism: Synechococcus elongatus
Length: 126 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMDFEDIYRFFQDPPPHYLSKELAVCYVLAVLRHEDSYGTELIQHLETHWPNYRLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQANDDRSRDLAQLWERYLSSSAATDRQLIPVEAR
UniProtKB AC: Q31QG0 (positions: 1-110)
Coverage: 87%
Name: Transcriptional regulator, PadR family
Source organism: Synechococcus elongatus
Length: 126 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMDFEDIYRFFQDPPPHYLSKELAVCYVLAVLRHEDSYGTELIQHLETHWPNYRLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQANDDRSRDLAQLWERYLSSSAATDRQLIPVEAR
UniProtKB AC: Q31QG0 (positions: 1-112)
Coverage: 88%
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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