The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane. The enzyme hydrolyzes a broad range of halogenated cyclic and aliphatic compounds. Here, we present the 1.58 A crystal structure of LinB and the 2.0 A structure of LinB with 1,3-propanediol, a product of debromination of 1,3-dibromopropane, in the active site of the enzyme. The enzyme belongs to the alpha/beta hydrolase family and contains a catalytic triad (Asp108, His272, and Glu132) in the lipase-like topological arrangement previously proposed from mutagenesis experiments. The LinB structure was compared with the structures of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 and from Rhodococcus sp. and the structural features involved in the adaptation toward xenobiotic substrates were identified. The arrangement and composition of the alpha-helices in the cap domain results in the differences in the size and shape of the active-site cavity and the entrance tunnel. This is the major determinant of the substrate specificity of this haloalkane dehalogenase.

BackgroundThe SMC5-6 protein complex is involved in the cellular response to DNA damage. It is composed of 6–8 polypeptides, of which Nse1, Nse3 and Nse4 form a tight sub-complex. MAGEG1, the mammalian ortholog of Nse3, is the founding member of the MAGE (melanoma-associated antigen) protein family and Nse4 is related to the EID (E1A-like inhibitor of differentiation) family of transcriptional repressors.Methodology/Principal FindingsUsing site-directed mutagenesis, protein-protein interaction analyses and molecular modelling, we have identified a conserved hydrophobic surface on the C-terminal domain of Nse3 that interacts with Nse4 and identified residues in its N-terminal domain that are essential for interaction with Nse1. We show that these interactions are conserved in the human orthologs. Furthermore, interaction of MAGEG1, the mammalian ortholog of Nse3, with NSE4b, one of the mammalian orthologs of Nse4, results in transcriptional co-activation of the nuclear receptor, steroidogenic factor 1 (SF1). In an examination of the evolutionary conservation of the Nse3-Nse4 interactions, we find that several MAGE proteins can interact with at least one of the NSE4/EID proteins.Conclusions/SignificanceWe have found that, despite the evolutionary diversification of the MAGE family, the characteristic hydrophobic surface shared by all MAGE proteins from yeast to humans mediates its binding to NSE4/EID proteins. Our work provides new insights into the interactions, evolution and functions of the enigmatic MAGE proteins.

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SUMMARYMultistep phosphorelay (MSP) signaling mediates responses to a variety of important stimuli in plants. In Arabidopsis MSP, the signal is transferred from sensor histidine kinase (HK) via histidine phosphotransfer proteins (AHP1-AHP5) to nuclear response regulators. In contrast to ancestral two-component signaling in bacteria, protein interactions in plant MSP are supposed to be rather nonspecific. Here, we show that the C-terminal receiver domain of HK CKI1 (CKI1 RD ) is responsible for the recognition of CKI1 downstream signaling partners, and specifically interacts with AHP2, AHP3 and AHP5 with different affinities. We studied the effects of Mg 2+ , the co-factor necessary for signal transduction via MSP, and phosphorylation-mimicking BeF 3 ) on CKI1 RD in solution, and determined the crystal structure of free CKI1 RD and CKI1 RD in a complex with Mg 2+ . We found that the structure of CKI1 RD shares similarities with the only known structure of plant HK, ETR1 RD , with the main differences being in loop L3. Magnesium binding induces the rearrangement of some residues around the active site of CKI1 RD , as was determined by both X-ray crystallography and NMR spectroscopy. Collectively, these results provide initial insights into the nature of molecular mechanisms determining the specificity of MSP signaling and MSP catalysis in plants.

An efficient water soluble fluorescent Al(3+) receptor, 1-[[(2-furanylmethyl)imino]methyl]-2-naphthol (1-H) was synthesized and characterized by physico-chemical and spectroscopic tools along with single crystal X-ray crystallography. High selectivity and affinity of 1-H towards Al(3+) in HEPES buffer (DMSO/water: 1/100) of pH 7.4 at 25 °C showed it to be suitable for detection of intracellular Al(3+) by fluorescence microscopy. Metal ions, viz. alkali (Na(+), K(+)), alkaline earth (Mg(2+), Ca(2+)), and transition-metal ions (Ni(2+), Zn(2+), Cd(2+), Co(2+), Cu(2+), Fe(3+), Cr(3+/6+), Hg(2+)) and Pb(2+), Ag(+) did not interfere. The lowest detection limit for Al(3+) was calculated to be 6.03 × 10(-7) M in 100 mM HEPES buffer (DMSO/water: 1/100). Theoretical calculations have also been included in support of the configuration of the probe-aluminium complex.

A prototypical study of NMR chemical shifts in biologically relevant heteroaromatic compounds containing a heavy halogen atom is presented for two isomers of halogen-substituted purines. Complete sets of (1)H-, (13)C- and (15)N-NMR chemical shifts are determined experimentally in solution. Experimental results are complemented by quantum-chemical calculations that provide understanding of the trends in the chemical shifts for the studied compounds and which show how different physical effects influence the NMR parameters. Chemical shifts for isolated molecules are calculated using density-functional theory methods, the role of solvent effects is studied using polarised continuum models, and relativistic corrections are calculated using the leading-order Breit-Pauli perturbation theory. Calculated values are compared with the experimental data and the effects of structure, solvent and relativity are discussed. Overall, we observe a good agreement of theory and experiment. We find out that relativistic effects cannot be neglected even in the chlorine species when aiming at high precision and a good agreement with the experimental data. Relativity plays a crucial role in the bromine and iodine species. Solvent effects are of smaller importance for (13)C shifts but are shown to be substantial for particular (15)N shifts. The test of method performance shows that the BLYP and B3LYP functionals provide the most reliable computational results after inclusion of the solvent and relativistic effects while BHandHLYP may--depending on atom in question--slightly improve but mostly deteriorate the data. Ab initio Hartree-Fock suffers from triplet instability in the Breit-Pauli relativistic part while MP2 provides no clear improvement over DFT in the nonrelativistic region. This work represents the first full application of the Breit-Pauli perturbation theory to an organic chemistry problem.

Some 8-substituted derivatives of the protoberberine alkaloids palmatine (1a) and berberine (1b) have been prepared and investigated by 1D and 2D NMR spectroscopy (H-1, C-13, N-15). Complete NMR data for the 8-hydroxy (2), 8-methoxy (3), 8-ethoxy (4), and 8-trichloromethyl (5) 7,8-dihydro derivatives of 1a and 1b, as well as X-ray data for 8-methoxydihydroberberine (3b), 8-trichloromethyldihydropalmatine (5a), and 8-trichloromethyldihydroberberine (5b), are presented. The physicochemical data for all of these compounds are reviewed and compared with previously published values.

1,1-Disubstituted-3-(2-phenyl-3H-quinazolin-4-ylidene)thioureas (8) were synthesized in a one pot reaction of N-(2-cyanophenyl)benzimidoyl isothicyanate (3) with secondary amines. The products underwent transamination reactions. Compounds 8a-8g were identified by FTIR, 1H-NMR, 13C-NMR, mass spectroscopy and X-ray crystallography.