9QBC | pdb_00009qbc

Crystal structure of Brachyspira hampsonii PadR

PDB DOI: https://doi.org/10.2210/pdb9QBC/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Brachyspira hampsonii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-02 Released: 2026-03-11
Deposition Author(s): Thunnissen, A.M.W.H., Rozeboom, H.J., Brouwer, B., Roelfes, G.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO), European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.277 (Depositor), 0.277 (DCC)
R-Value Work:
0.225 (Depositor), 0.225 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Exploring PadR Proteins for Artificial Enzyme Design.

Brouwer, B., Thunnissen, A.W.H., Rozeboom, H.J., Roelfes, G.

(2026) Chembiochem 27: e70308-e70308

PubMed: 42047317 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/cbic.70308
Primary Citation Related Structures:
9QBC, 9QBD

PubMed Abstract:
The development of artificial enzymes through incorporation of new-to-nature catalytic functionality into protein scaffolds has emerged as a powerful approach to expand the biocatalytic repertoire. Inspired by the success of Lactococcal multidrug resistance regulator (LmrR), a transcriptional regulator protein, whose unique scaffold has been used for the design of a range of artificial enzymes, we performed a bioinformatics study in an effort to expand the scope of protein scaffolds for artificial enzyme design with other LmrR-like proteins. LmrR belongs to the phenolic acid decarboxylase transcriptional regulator (PadR) subfamily 2 (PadR-s2) and exhibits an unusual open pore with promiscuous binding capabilities. Using genome mining and homology modeling, we identified six previously uncharacterized PadR-s2 proteins and experimentally evaluated them as protein scaffolds for the design of artificial Friedel-Crafts (FC) alkylases. Two of the candidates, Lactococcus fujiensis (LCf) PadR and Brachyspirahampsonii (Bh) PadR, could be applied in the iminium-promoted FC-alkylation using genetically incorporated noncanonical amino acids p-aminophenylalanine or 3-aminotyrosine as catalytic residues. Interestingly, contrary to homology models, AlphaFold predictions of the PadR-s2 candidates and X-ray crystallography of BhPadR and a variant incorporating 3-aminotyrosine revealed closed-pore structures. Our findings thus demonstrate that an open-pore structure like LmrR is not a prerequisite for designing artificial FC-alkylases and introduce two new PadR-s2 scaffolds for future application.