Database accession: MF7000139
Name: AphA (Vibrio cholerae)
PDB ID: 1yg2
Experimental method: X-ray (2.20 Å)
Assembly: Homodimer
Source organism: Vibrio cholerae
Primary publication of the structure:
De Silva RS, Kovacikova G, Lin W, Taylor RK, Skorupski K, Kull FJ
Crystal structure of the virulence gene activator AphA from Vibrio cholerae reveals it is a novel member of the winged helix transcription factor superfamily.
(2005) J. Biol. Chem. 280: 13779-83
PMID: 15647287
Abstract:
AphA is a member of a new and largely uncharacterized family of transcriptional activators that is required for initiating virulence gene expression in Vibrio cholerae, the causative agent of the frequently fatal epidemic diarrheal disease cholera. AphA activates transcription by an unusual mechanism that appears to involve a direct interaction with the LysR-type regulator AphB at the tcpPH promoter. As a first step toward understanding the molecular basis for tcpPH activation by AphA and AphB, we have determined the crystal structure of AphA to 2.2 angstrom resolution. AphA is a dimer with an N-terminal winged helix DNA binding domain that is architecturally similar to that of the MarR family of transcriptional regulators. Unlike this family, however, AphA has a unique C-terminal antiparallel coiled coil domain that serves as its primary dimerization interface. AphA monomers are highly unstable by themselves and form a linked topology, requiring the protein to partially unfold to form the dimer. The structure of AphA also provides insights into how it cooperates with AphB to activate transcription, most likely by forming a heterotetrameric complex at the tcpPH promoter.
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, 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
Source organism: Vibrio cholerae
Length: 179 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSLPHVILTVLSTRDATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSALGEWFDQPTAHPTVRDEFSAKLMACSVQSAEPYRLQLAELVEESRKLVAHYQEIEAAYYANPAVLDKQQRLERLTLRRNLLVRQAWIQWADEVLAELNAMA
UniProtKB AC: Q9X399 (positions: 2-179)
Coverage: 99%
Name: Transcriptional regulator
Source organism: Vibrio cholerae
Length: 179 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSLPHVILTVLSTRDATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSALGEWFDQPTAHPTVRDEFSAKLMACSVQSAEPYRLQLAELVEESRKLVAHYQEIEAAYYANPAVLDKQQRLERLTLRRNLLVRQAWIQWADEVLAELNAMA
UniProtKB AC: Q9X399 (positions: 2-179)
Coverage: 99%
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 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)
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