Crystal structure of PqqB from Pseudomonas putida at 2.2 Å resolution

Moritz Metlitzky, Sandra Puehringer, Stuart J. Fisher

Department of Molecular Biology, University of Salzburg, Salzburg, Austria.

DOI: 10.4236/jbpc.2012.32023                

Abstract

Pyrroloquinoline quinone (PQQ) is an important redox-active cofactor for many bacterial dehy-drogenases. It's biosynthetic pathway involves six or seven genes, one of which is pqqB. Former studies indicated that the protein encoded by pqqB, namely PqqB, functions as a PQQ transporter. Here we report the crystal structure of PqqB from Pseudomonas putida at 2.2 ? resolution together with functional studies to verify this theory.

Keywords

PqqB; PQQ; Biosynthetic Pathway; X-Ray Crystallography

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Anthony, C. (2001) Pyrroloquinoline quinone (pqq) and quinoprotein enzymes. Antioxidants & Redox Signaling, 3, 757-774. doi:10.1089/15230860152664966
[2]	Stites, T.E., Mitchell, A.E. and Rucker, R.B. (2000) Physiological importance of quinoenzymes and the o-quinone family of cofactors. The Journal of Nutrition, 130, 719-727.
[3]	Zhang, Y. and Rosenberg, P.A. (2002) The essential nutrient pyrroloquinoline quinone may act as a neuroprotectant by suppressing peroxynitrite formation. European Journal of Neuroscience, 16, 1015-1024. doi:10.1046/j.1460-9568.2002.02169.x
[4]	Felton, L.M. and Anthony, C. (2005) Biochemistry: Role of PQQ as a mammalian enzyme cofactor? Nature, 433, E10-E10. doi:10.1038/nature03322
[5]	Rucker, R., Storms, D., Sheets, A., Tchaparian, E. and Fascetti, A. (2005) Biochemistry: Is pyrroloquinoline quinone a vitamin? Nature, 433, E10-E11. doi:10.1038/nature03323
[6]	Meulenberg, J.J.M., Sellink, E., Riegman, N.H. and Postma, P.W. (1992) Nucleotide sequence and structure of the klebsiella pneumoniae pqq-operon. Molecular and General Genetics MGG, 232, 284-294.
[7]	Goosen, N., Huinen, R.G. and Van de Putte, P. (1992) A 24-amino-acid polypeptide is essential for the biosynthesis of the coenzyme pyrrolo-quinoline-quinone. Journal of Bacteriology, 174, 1426-1427.
[8]	Goosen, N., Horsman, H.P., Huinen, R.G. and Van de Putte, P. (1989) Acinetobacter calcoaceticus genes involved in biosynthesis of the coenzyme pyrrolo-quinoline-quinone: Nucleotide sequence and expression in escherichia coli k-12. Journal of Bacteriology, 171, 447-455.
[9]	Velterop, J.S., et al. (1995) Synthesis of pyrroloquinoline quinone in-vivo and in-vitro and detection of an intermediate in the biosynthetic-pathway. Journal of Bacteriology, 177, 5088-5098.
[10]	Aizenman, E., Hartnett, K., Zhong, C., Gallop, P. and Rosenberg, P. (1992) Interaction of the putative essential nutrient pyrroloquinoline quinone with the n-methyl-d-aspartate receptor redox modulatory site. The Journal of Neuroscience, 12, 2362-2369.
[11]	Magnusson, O.T., et al. (2004) Quinone biogenesis: Structure and mechanism of PqqC, the final catalyst in the production of pyrroloquinoline quinone. Proceedings of the National Academy of Sciences of the United States of America, 101, 7913-7918. doi:10.1073/pnas.0402640101
[12]	Harding, M. (2004) The architecture of metal coordination groups in proteins. Acta Crystallographica Section D, 60, 849-859. doi:10.1107/S0907444904004081
[13]	Hegg, E.L. and Jr, L.Q. (1997) The 2-his-1-carboxylate facial triad—An emerging structural motif in mononuclear non-heme iron(ii) enzymes. European Journal of Biochemistry, 250, 625-629. doi:10.1111/j.1432-1033.1997.t01-1-00625.x
[14]	Seedorf, H., et al. (2007) Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic archaea catalyzing the reduction of O2 to H2O. FEBS Journal, 274, 1588-1599. doi:10.1111/j.1742-4658.2007.05706.x
[15]	Tsai, T.-Y., Yang, C.-Y., Shih, H.-L., Wang, A.H.J. and Chou, S.-H. (2009) Xanthomonas campestris PqqD in the pyrroloquinoline quinone biosynthesis operon adopts a novel saddle-like fold that possibly serves as a PQQ carrier. Proteins: Structure, Function, and Bioinformatics, 76, 1042-1048. doi:10.1002/prot.22461
[16]	Jaroszewski, L., Rychlewski, L., Li, Z., Li, W. and Godzik, A. (2005) FFAS03: A server for profile—profile sequence alignments. Nucleic Acids Research, 33, W284-W288.
[17]	Laskowski, R.A., Watson, J.D. and Thornton, J.M. (2005) Protein function prediction using local 3D templates. Journal of Molecular Biology, 351, 614-626. doi:10.1016/j.jmb.2005.05.067
[18]	Sippl, M.J. (2008) On distance and similarity in fold space. Bioinformatics, 24, 872-873. doi:10.1093/bioinformatics/btn040
[19]	Sippl, M.J. and Wiederstein, M. (2008) A note on difficult structure alignment problems. Bioinformatics, 24, 426-427. doi:10.1093/bioinformatics/btm622
[20]	Mueller, U., et al. (2012) Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin, Journal of Synchrotron Radiation, 19, 442-449.
[21]	Otwinowski, Z. and Minor, W. (1997) Processing of x-ray diffraction data collected in oscillation mode. Methods in Enzymology, 276, 307-326. doi:10.1016/S0076-6879(97)76066-X
[22]	Vagin, A.A. and Teplyakov, A. (1997) Molrep: An automated program for molecular replacement. Journal of Applied Crystallography, 30, 1022-1025. doi:10.1107/S0021889897006766
[23]	Murshudov, G.N., Vagin, A.A. and Dodson, E.J. (1997) Refinement of macromolecular structures by the maxi-mumlikelihood method. Acta Crystallographica Section D, 53, 240-255. doi:10.1107/S0907444996012255
[24]	Emsley, P. and Cowtan, K. (2004) Coot: Model-building tools for molecular graphics. Acta Crystallographica Section D Biological Crystallography, 60, 2126-2132. doi:10.1107/S0907444904019158
[25]	DeLano, W.L. (2002) The PyMol molecular graphics system. http://www.pymol.org