Database accession: MF7000669
Name: VanR with vanillate
PDB ID: 6lg2
Experimental method: X-ray (1.60 Å)
Assembly: Homodimer
Source organism: Corynebacterium glutamicum
Primary publication of the structure:
Yao J, He Y, Su N, Bharath SR, Tao Y, Jin JM, Chen W, Song H, Tang SY
Developing a highly efficient hydroxytyrosol whole-cell catalyst by de-bottlenecking rate-limiting steps.
(2020) Nat Commun 11: 1515
PMID: 32251291
Abstract:
Hydroxytyrosol is an antioxidant free radical scavenger that is biosynthesized from tyrosine. In metabolic engineering efforts, the use of the mouse tyrosine hydroxylase limits its production. Here, we design an efficient whole-cell catalyst of hydroxytyrosol in Escherichia coli by de-bottlenecking two rate-limiting enzymatic steps. First, we replace the mouse tyrosine hydroxylase by an engineered two-component flavin-dependent monooxygenase HpaBC of E. coli through structure-guided modeling and directed evolution. Next, we elucidate the structure of the Corynebacterium glutamicum VanR regulatory protein complexed with its inducer vanillic acid. By switching its induction specificity from vanillic acid to hydroxytyrosol, VanR is engineered into a hydroxytyrosol biosensor. Then, with this biosensor, we use in vivo-directed evolution to optimize the activity of tyramine oxidase (TYO), the second rate-limiting enzyme in hydroxytyrosol biosynthesis. The final strain reaches a 95% conversion rate of tyrosine. This study demonstrates the effectiveness of sequentially de-bottlenecking rate-limiting steps for whole-cell catalyst development.
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)
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