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1.  Purification, crystallization and preliminary crystallographic analysis of banyan peroxidase 
Crystals of a new peroxidase, named banyan peroxidase, from the latex of F. benghalensis belonged to the trigonal space group P3221 and provided X-ray diffraction data to a resolution of 1.66 Å. The anomalous signal of the intrinsic iron and calcium ions was sufficent for phasing by SAD.
Plant peroxidases are extensively used in a wide range of biotechnological applications owing to their high environmental and thermal stability. A new peroxidase, named banyan peroxidase, was purified from the latex of Ficus benghalensis and crystallized. X-ray diffraction data were collected from native crystals and from bromide and xenon derivatives to resolutions of up to 1.66 Å in the trigonal space group P3221, with unit-cell parameters a = b = 73.1, c = 164.6 Å. The anomalous signal of the intrinsic iron and calcium ions was sufficient for structure solution by SAD, although the sequence is not yet known.
doi:10.1107/S1744309112026097
PMCID: PMC3412776  PMID: 22869125
plant peroxidases; Ficus benghalensis; latex
2.  Crystallization and preliminary X-ray diffraction studies of the putative haloalkane dehalogenase DppA from Plesiocystis pacifica SIR-I 
The crystallization and preliminary X-ray diffraction studies of DppA from P. pacifica SIR-I are reported.
DppA from Plesiocystis pacifica SIR-I is a putative haloalkane dehalogenase (EC 3.8.1.5) and probably catalyzes the conversion of halogenated alkanes to the corresponding alcohols. The enzyme was expressed in Escherichia coli BL21 and purified to homogeneity by ammonium sulfate precipitation and reversed-phase and ion-exchange chromatography. The DppA protein was crystallized by the vapour-diffusion method and protein crystals suitable for data collection were obtained in the orthorhombic space group P21212. The DppA crystal diffracted X-rays to 1.9 Å resolution using an in-house X-ray generator.
doi:10.1107/S1744309110018932
PMCID: PMC2898472  PMID: 20606284
haloalkane dehalogenases; Plesiocystis pacifica SIR-I
3.  Crystallization and preliminary X-ray crystallographic analysis of the tetracycline-degrading monooxygenase TetX2 from Bacteroides thetaiotaomicron  
Crystallization and preliminary X-ray crystallographic analysis of the tetracycline-degrading monooxygenase TetX2 from B. thetaiotaomicron are reported.
The flavin-dependent monooxygenase TetX2 from Bacteroides thetaiotaomicron confers resistance against tetracyclines in aerobically grown Escherichia coli. TetX2 modifies several tetracycline antibiotics by regioselective hydroxylation of the substrates to 11a-hydroxy-tetracyclines. X-ray diffraction data were collected from a native TetX2 crystal and a TetX2 crystal with incorporated selenomethionine to resolutions of 2.5 and 3.0 Å, respectively. The native crystal belonged to the triclinic space group P1, with unit-cell parameters a = 68.55, b = 80.88, c = 87.53 Å, α = 111.09, β = 98.98, γ = 93.38°, whereas the selenomethionine-labelled TetX2 crystal belonged to the monoclinic space group P21, with unit-cell parameters a = 87.34, b = 68.66, c = 152.48 Å, β = 101.08°.
doi:10.1107/S174430911001225X
PMCID: PMC2864705  PMID: 20445272
tetracycline resistance; tetracycline degradation; flavin-dependent monooxygenases; Bacteroides thetaiotaomicron
4.  Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR 
Nucleic Acids Research  2012;40(9):4178-4192.
Bacillus subtilis encodes redox-sensing MarR-type regulators of the OhrR and DUF24-families that sense organic hydroperoxides, diamide, quinones or aldehydes via thiol-based redox-switches. In this article, we characterize the novel redox-sensing MarR/DUF24-family regulator HypR (YybR) that is activated by disulphide stress caused by diamide and NaOCl in B. subtilis. HypR controls positively a flavin oxidoreductase HypO that confers protection against NaOCl stress. The conserved N-terminal Cys14 residue of HypR has a lower pKa of 6.36 and is essential for activation of hypO transcription by disulphide stress. HypR resembles a 2-Cys-type regulator that is activated by Cys14–Cys49′ intersubunit disulphide formation. The crystal structures of reduced and oxidized HypR proteins were resolved revealing structural changes of HypR upon oxidation. In reduced HypR a hydrogen-bonding network stabilizes the reactive Cys14 thiolate that is 8–9 Å apart from Cys49′. HypR oxidation breaks these H-bonds, reorients the monomers and moves the major groove recognition α4 and α4′ helices ∼4 Å towards each other. This is the first crystal structure of a redox-sensing MarR/DUF24 family protein in bacteria that is activated by NaOCl stress. Since hypochloric acid is released by activated macrophages, related HypR-like regulators could function to protect pathogens against the host immune defense.
doi:10.1093/nar/gkr1316
PMCID: PMC3351151  PMID: 22238377
5.  Structure of the apo form of the catabolite control protein A (CcpA) from Bacillus megaterium with a DNA-binding domain 
Crystal structure analysis of the apo form of catabolite control protein A reveals the three-helix bundle of the DNA-binding domain. In the crystal packing, this domain interacts with the binding site for the corepressor protein.
Crystal structure determination of catabolite control protein A (CcpA) at 2.6 Å resolution reveals for the first time the structure of a full-length apo-form LacI-GalR family repressor protein. In the crystal structures of these transcription regulators, the three-helix bundle of the DNA-binding domain has only been observed in cognate DNA complexes; it has not been observed in other crystal structures owing to its mobility. In the crystal packing of apo-CcpA, the protein–protein contacts between the N-terminal three-helix bundle and the core domain consisted of interactions between the homodimers that were similar to those between the corepressor protein HPr and the CcpA N-subdomain in the ternary DNA complex. In contrast to the DNA complex, the apo-CcpA structure reveals large subdomain movements in the core, resulting in a complete loss of contacts between the N-subdomains of the homodimer.
doi:10.1107/S1744309107008949
PMCID: PMC2330204  PMID: 17401189
catabolite control protein A; carbon catabolite repression; Bacillus megaterium

Results 1-5 (5)