Database accession: MF7000663
Name: VanR transcription factor with vanillate
PDB ID: 5z7b
Experimental method: X-ray (2.10 Å)
Assembly: Homodimer
Source organism: Corynebacterium glutamicum
Primary publication of the structure:
Kwak YM, Park SC, Na HW, Kang SG, Lee GS, Ko HJ, Kim PH, Oh BC, Yoon SI
Crystal structure of the VanR transcription factor and the role of its unique α-helix in effector recognition.
(2018) FEBS J. 285: 3786-3800
PMID: 30095229
Abstract:
VanR is a negative transcriptional regulator of bacteria that belongs to the PadR family and modulates the expression of vanillate transport and degradation proteins in response to vanillate. Although VanR plays a key role in the utilization of vanillate as a carbon source, it is barely understood how VanR recognizes its effector. Thus, our knowledge concerning the gene regulatory mechanism of VanR is limited. Here, we reveal the vanillate-binding mode of VanR through structural, biophysical, and mutational studies. Similar to other PadR family members, VanR forms a functional dimer, and each VanR subunit consists of an N-terminal DNA-binding domain (NTD) and a C-terminal dimerization domain (CTD). One VanR dimer simultaneously binds two vanillate molecules using two interdomain cavities, as observed in PadR. In contrast to these common features, VanR contains an additional α-helix, αi, that has not been found in other PadR family members. The αi helix functions as an interdomain crosslinker that mediates interactions between the NTD and the CTD. In addition, the VanR-specific αi helix plays a key role in the formation of a unique effector-binding site. As a result, the effector-binding mode of VanR is distinguishable from that of PadR in the location and accessibility of the effector-binding site as well as the orientation of its bound effector. Furthermore, we propose the DNA-binding mode and vanillate-mediated transcriptional regulation mechanism of VanR based on comparative structural and mutational analyses. DATABASES: The atomic coordinates and the structure factors for VanR (PDB ID 5Z7B) have been deposited in the Protein Data Bank, www.pdb.org.
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: Predicted transcriptional regulators
Source organism: Corynebacterium glutamicum
Length: 192 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTLRSALLALLSSGPLTGYDASQRFGASVGFVWSGSDSQIYPELRKMEAEELLVGSDVPWGSKGATKTEYALSEKGWEALRKAWYEPVTYGPTRDPARLKAAYFEVGTNGDARRHLRAHIAHFEQQKIQSESMIDELKAKTHPTLARRLERSPKKEHERIVAFKVLAYEGQIARAQAEIEWAEKGLKLLDTL
UniProtKB AC: Q8NN31 (positions: 1-192)
Coverage: 100%
Name: Predicted transcriptional regulators
Source organism: Corynebacterium glutamicum
Length: 192 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTLRSALLALLSSGPLTGYDASQRFGASVGFVWSGSDSQIYPELRKMEAEELLVGSDVPWGSKGATKTEYALSEKGWEALRKAWYEPVTYGPTRDPARLKAAYFEVGTNGDARRHLRAHIAHFEQQKIQSESMIDELKAKTHPTLARRLERSPKKEHERIVAFKVLAYEGQIARAQAEIEWAEKGLKLLDTL
UniProtKB AC: Q8NN31 (positions: 1-192)
Coverage: 100%
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)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
