Crystal structure of the dimeric, isolated VapC toxin from Shigella flexneri (Xu et al., Proteins, 2016).

Today, our lab published a comprehensive, structural analysis of the active site configuration observed in the Shigella flexneri VapC toxin RNase. By comparison to bacterial RNase H, we show that there are in up to five residues that are conserved in the active site, and not three as has previously been believed. We are also able to model substrate in the active site by analogy to RNase H, providing a first glimpse at what the molecular mechanism of catalysis might be for the PIN domain bacterial RNases.

For more information, have a look at the paper in Proteins.

Xu K., Dedic E., and Brodersen D. E. (2016) “Structural analysis on the active site architecture of the VapC toxin from Shigella flexneri”, Proteins, 84(7):892-899.

Crystal structure of the Qbeta holo complex bound to ribosomal protein S1

Today, our lab in collaboration with the labs of Charlotte Knudsen and Frans Mulder, published a paper describing crystal and NMR structural studies of the Qbeta replicase holo complex bound to ribosomal protein S1. In the paper, we show how S1 interacts with the viral replicase along with the two other host proteins, elongation factors EF-Tu and EF-Ts, to generate the fully functional, viral replicase enzyme. Using NMR, we further show how  two of the OB domains of S1 are involved in binding viral RNA during replication.

For more information, have a look at the paper in Nucleic Acids Research.

Gytz, H., Mohr, D., Seweryn, P., Yoshimura, Y., Kutlubaeva, Z., Dolman, F., Chelchessa, B., Chetverin, A. B., Mulder, F. A. A., Brodersen, D. E. and Knudsen, C. R. (2015) ” Structural basis for RNA-genome recognition during bacteriophage Qβ replication”, Nucleic Acids Res, 43(22):10893-906.

Regions involved in conferring substrate specificity among fungal NRPS A domains

Today, our lab in collaboration with the lab of Christian Storm Pedersen at the BiRC bioinformatics centre, published a paper in Bioinformatics describing a novel computational analysis of the substrate conferring code of fungal non-ribosomal peptide synthetase (NRPS) A domains, which are responsible for recognising and activating the individual amino acid substrates during peptide synthesis. We can show that a much larger part of the A domain than hitherto imagined is involved in conferring substrate specificity, and could map this to the structure of the A domain.

For more information, have a look at the paper in Bioinformatics.

Knudsen, M., Søndergaard, D., Tofting-Olesen, C., Hansen, F.,T., Brodersen, D. E., Pedersen, C. N. (2015) “Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases”, Bioinformatics, 32(3):325-9.

Crystal structure of the C-P lyase core complex determined by x-ray crystallography

Today, our lab published a full article in Nature describing the crystal structure of a 240 kDa core complex of the E. coli C-P lyase, an enzyme required for utilisation of phosphonate compounds in bacteria. Phosphonate are characterised by a direct  carbon-phosphorus (C-P) bond, which is stable to  hydrolysis and therefore requires a totally different enzymatic machinery. In C-P lyase, cleavage of the bond is achieved using radical chemistry in the subunit PhnJ, which is one of four proteins in the hetero-octameric core complex. We also show, using negative stain electron microscopy, that a fifth subunit, PhnK, an ABC cassette protein, binds as a monomer to the core complex via a conserved loop in PhnJ and breaks the two-fold symmetry of the core.

For more information, have a look at the paper in Nature.

Seweryn, P., Van, L. B., Kjeldgaard, M., Russo, C. J., Passmore, L. A., Hove-Jensen, B., Jochimsen, B., Brodersen, D. E. (2015) “Structural insights into the bacterial carbon-phosphorus lyase machinery”, Nature, 525(7567): 68-72.

Structures of the THO complex components Mft1p and Thp2p

Today, our lab published a comprehensive analysis of the yeast THO complex by small-angle x-ray scattering in the open access journal, PLoS One. The THO complex is intimately involved in coupling transcription to downstream mRNP processing and export from the nucleus. In the paper, we dissect the architecture of the complex through purification of sub complexes and structure determination of these by SAXS. Putting the pieces together reveals the position of each of the 5 proteins in the core complex and opens up new possibilities for a functional understanding of the complex.

For more information, have a look at the paper in PLoS One.

Poulsen J. B., Sanderson L. E., Agerschou E. D., Dedic E., Boesen T., Brodersen D. E. (2014), “Structural Characterization of the Saccharomyces cerevisiae THO Complex by Small-Angle X-Ray Scattering”, PLoS One, 9(7):e103470.

Structure of the Rrp6p-Rrp47p complex by SAXS

Today, our lab has published structural and functional studies of the yeast exosome Rrp6p-Rrp47p complex in Biochem. Biophys. Res. Commun. In this paper, we show how the two proteins, despite the fact that they both multimerise, form a stable 1:1 complex with Rrp47p situated on the “top” of the Rrp6p exonuclease domain. RNA degradation experiments with and without Rrp47p present further show that the co-factor has a very limited effect on the activity and specificity of the nuclease. Together, our data suggest a role for Rrp47p in higher-order organisation of the exosome complex, perhaps linked to interactions with other protein factors.

For more information, have a look at the paper in Biochem. Biophys. Res. Commun.