Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis.

Amino Acid Sequence; Crystallography, X-Ray; Escherichia coli Proteins/chemistry/metabolism; Models, Biological; Molecular Sequence Data; Peptidoglycan/biosynthesis/metabolism; Phosphoric Monoester Hydrolases/chemistry/metabolism; Polyisoprenyl Phosphates/chemistry/metabolism; Protein Structure, Secondary; Pyrophosphatases/chemistry/metabolism

Abstract :

[en] As a protective envelope surrounding the bacterial cell, the peptidoglycan sacculus is a site of vulnerability and an antibiotic target. Peptidoglycan components, assembled in the cytoplasm, are shuttled across the membrane in a cycle that uses undecaprenyl-phosphate. A product of peptidoglycan synthesis, undecaprenyl-pyrophosphate, is converted to undecaprenyl-phosphate for reuse in the cycle by the membrane integral pyrophosphatase, BacA. To understand how BacA functions, we determine its crystal structure at 2.6 A resolution. The enzyme is open to the periplasm and to the periplasmic leaflet via a pocket that extends into the membrane. Conserved residues map to the pocket where pyrophosphorolysis occurs. BacA incorporates an interdigitated inverted topology repeat, a topology type thus far only reported in transporters and channels. This unique topology raises issues regarding the ancestry of BacA, the possibility that BacA has alternate active sites on either side of the membrane and its possible function as a flippase.

Disciplines :

Biochemistry, biophysics & molecular biology

Author, co-author :

El Ghachi, Meriem ; Université de Liège > Département des sciences de la vie > Cristallographie des macromolécules biologiques

Howe, Nicole

Huang, Chia-Ying

Olieric, Vincent

Warshamanage, Rangana

Touze, Thierry

Weichert, Dietmar

Stansfeld, Phillip J.

Wang, Meitian

Kerff, Frédéric ; Université de Liège - ULiège > Département des sciences de la vie > Centre d'ingénierie des protéines

Caffrey, Martin

Language :

English

Title :

Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis.

Publication date :

2018

Journal title :

Nature Communications

eISSN :

2041-1723

Publisher :

Nature Publishing Group, United Kingdom

Volume :

Issue :

Pages :

1078

Peer reviewed :

Peer Reviewed verified by ORBi

Available on ORBi :

since 27 June 2018

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Bibliography

Vollmer, W., Blanot, D. & de Pedro, M. A. Peptidoglycan structure and architecture. FEMS Microbiol. Rev. 32, 149-167 (2008).
Mohammad, H. et al. Phenylthiazole antibacterial agents targeting cell wall synthesis exhibit potent activity in vitro and in vivo against vancomycinresistant Enterococci. J. Med. Chem. 60, 2425-2438 (2017).
Wang, Y. et al. Bacterial cell growth inhibitors targeting undecaprenyl diphosphate synthase and undecaprenyl diphosphate phosphatase. ChemMedChem 11, 2311-2319 (2016).
Barreteau, H. et al. Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol. Rev. 32, 168-207 (2008).
Manat, G. et al. Deciphering the metabolism of undecaprenyl-phosphate: the bacterial cell-wall unit carrier at the membrane frontier. Microb. Drug Resist. 20, 199-214 (2014).
El Ghachi, M., Bouhss, A., Blanot, D. & Mengin-Lecreulx, D. The bacA gene of Escherichia coli encodes an undecaprenyl pyrophosphate phosphatase activity. J. Biol. Chem. 279, 30106-30113 (2004).
Ruiz, N. Lipid flippases for bacterial peptidoglycan biosynthesis. Lipid Insights 8, 21-31 (2015).
Sham, L. T. et al. Bacterial cell wall. MurJ is the flippase of lipid-linked precursors for peptidoglycan biogenesis. Science 345, 220-222 (2014).
Meeske, A. J. et al. SEDS proteins are a widespread family of bacterial cell wall polymerases. Nature 537, 634-638 (2016).
Mohammadi, T. et al. Identification of FtsW as a transporter of lipid-linked cell wall precursors across the membrane. EMBO J. 30, 1425-1432 (2011).
Apfel, C. M., Takacs, B., Fountoulakis, M., Stieger, M. & Keck, W. Use of genomics to identify bacterial undecaprenyl pyrophosphate synthetase: cloning, expression, and characterization of the essential uppS gene. J. Bacteriol. 181, 483-492 (1999).
El Ghachi, M., Derbise, A., Bouhss, A. & Mengin-Lecreulx, D. Identification of multiple genes encoding membrane proteins with undecaprenyl pyrophosphate phosphatase (UppP) activity in Escherichia coli. J. Biol. Chem. 280, 18689-18695 (2005).
Lu, Y. H., Guan, Z., Zhao, J. & Raetz, C. R. Three phosphatidylglycerolphosphate phosphatases in the inner membrane of Escherichia coli. J. Biol. Chem. 286, 5506-5518 (2011).
Touzé, T., Blanot, D. & Mengin-Lecreulx, D. Substrate specificity and membrane topology of Escherichia coli PgpB, an undecaprenyl pyrophosphate phosphatase. J. Biol. Chem. 283, 16573-16583 (2008).
Fan, J., Jiang, D., Zhao, Y., Liu, J. & Zhang, X. C. Crystal structure of lipid phosphatase Escherichia coli phosphatidylglycerophosphate phosphatase B. Proc. Natl. Acad. Sci. U. S. A. 111, 7636-7640 (2014).
Tong, S. et al. Structural insight into substrate selection and catalysis of lipid phosphate phosphatase PgpB in the cell membrane. J. Biol. Chem. 291, 18342-18352 (2016).
Chalker, A. F. et al. The bacA gene, which determines bacitracin susceptibility in Streptococcus pneumoniae and Staphylococcus aureus, is also required for virulence. Microbiology 146, 1547-1553 (2000).
Manat, G. et al. Membrane topology and biochemical characterization of the Escherichia coli BacA undecaprenyl-pyrophosphate phosphatase. PLoS One 10, e0142870 (2015).
Chang, H. Y., Chou, C. C., Hsu, M. F. & Wang, A. H. Proposed carrier lipidbinding site of undecaprenyl pyrophosphate phosphatase from Escherichia coli. J. Biol. Chem. 289, 18719-18735 (2014).
Caffrey, M. & Cherezov, V. Crystallizing membrane proteins using lipidic mesophases. Nat. Protoc. 4, 706-731 (2009).
Huang, C. Y. et al. In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Acta Crystallgr. D Struct. Biol. 72, 93-112 (2016).
von Heijne, G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol. 225, 487-494 (1992).
Holm, L. & Rosenstrom, P. Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, W545-W549 (2010).
Ovchinnikov, S. et al. Large-scale determination of previously unsolved protein structures using evolutionary information. Elife 4, e09248 (2015).
Li, D. et al. Crystallizing membrane proteins in the lipidic mesophase. Experience with human prostaglandin E2 synthase 1 and an evolving strategy. Cryst. Growth Des. 14, 2034-2047 (2014).
Petrou, V. I. et al. Structures of aminoarabinose transferase ArnT suggest a molecular basis for lipid A glycosylation. Science 351, 608-612 (2016).
Forrest, L. R. Structural symmetry in membrane proteins. Annu. Rev. Biophys. 44, 311-337 (2015).
Forrest, L. R. et al. Mechanism for alternating access in neurotransmitter transporters. Proc. Natl. Acad. Sci. USA 105, 10338-10343 (2008).
Stockbridge, R. B. et al. Crystal structures of a double-barrelled fluoride ion channel. Nature 525, 548-551 (2015).
Wojdyla, J. A. et al. Fast two-dimensional grid and transmission X-ray microscopy scanning methods for visualizing and characterizing protein crystals. J. Appl. Crystallogr. 49, 944-952 (2016).
Kabsch, W. Xds. Acta Crystallogr. D Biol. Crystallogr. 66, 125-132 (2010).
Sheldrick, G. M. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D Biol. Crystallogr. 66, 479-485 (2010).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallgr. D Biol. Crystallogr. 60, 2126-2132 (2004).
Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58, 1948-1954 (2002).
Bricogne, G. Direct phase determination by entropy maximization and likelihood ranking: status report and perspectives. Acta Crystallogr. D Biol. Crystallogr. 49, 37-60 (1993).
Roversi, P., Blanc, E., Vonrhein, C., Evans, G. & Bricogne, G. Modelling prior distributions of atoms for macromolecular refinement and completion. Acta Crystallogr. D Biol. Crystallogr. 56, 1316-1323 (2000).
Delano, W. L. The PyMOL Molecular Graphics System, Version 1.3, http:// pymol.org (Schrödinger, LLC, 2010).
Sali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815 (1993).
Bernsel, A., Viklund, H., Hennerdal, A. & Elofsson, A. TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res. 37, W465-W468 (2009).
Nugent, T. & Jones, D. T. Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics 10, 159 (2009).
Nugent, T. & Jones, D. T. Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics 14, 276 (2013).
Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1-2, 19-25 (2015).
de Jong, D. H. et al. Improved parameters for the Martini coarse-grained protein force field. J. Chem. Theory Comput. 9, 687-697 (2013).
Stansfeld, P. J. et al. MemProtMD: Automated insertion of membrane protein structures into explicit lipid membranes. Structure 23, 1350-1361 (2015).
Stansfeld, P. J. & Sansom, M. S. P. From coarse grained to atomistic: A serial multiscale approach to membrane protein simulations. J. Chem. Theory Comput. 7, 1157-1166 (2011).
Jefferys, E., Sands, Z. A., Shi, J., Sansom, M. S. & Fowler, P. W. Alchembed: A computational method for incorporating multiple proteins into complex lipid geometries. J. Chem. Theory Comput. 11, 2743-2754 (2015).
Oostenbrink, C., Villa, A., Mark, A. E. & Van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25, 1656-1676 (2004).
Malde, A. K. et al. An automated force field topology builder (ATB) and repository: Version 1.0. J. Chem. Theory Comput. 7, 4026-4037 (2011).
Hansson, T., Nordlund, P. & Aqvist, J. Energetics of nucleophile activation in a protein tyrosine phosphatase. J. Mol. Biol. 265, 118-127 (1997).
Li, D. et al. Ternary structure reveals mechanism of a membrane diacylglycerol kinase. Nat. Commun. 6, 10140 (2015).
Sondergaard, C. R., Olsson, M. H., Rostkowski, M. & Jensen, J. H. Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values. J. Chem. Theory Comput. 7, 2284-2295 (2011).
Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys. 126, 014101 (2007).
Parrinello, M. Polymorphic transitions in single-crystals-A new moleculardynamics method. J. Appl. Phys. 52, 7182-7190 (1981).
Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije J. G. E.M. LINCS: A linear constraint solver for molecular simulation. J. Comput. Chem. 18, 1463-1472 (1997).
Darden, T., York, D. & Pedersen, L. Particle mesh Ewald-An N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089-10092 (1993).
Páll, S. & Hess, B. A flexible algorithm for calculating pair interactions on SIMD architectures. Comput. Phys. Commun. 184, 2640-2650 (2003).
Michaud-Agrawal, N., Denning, E. J., Woolf, T. B. & Beckstein, O. MD Analysis: a toolkit for the analysis of molecular dynamics simulations. J. Comput. Chem. 32, 2319-2327 (2011).
Finn, R. D. et al. HMMER web server: 2015 update. Nucleic Acids Res. 43, W30-W38 (2015).
Ovchinnikov, S. et al. Protein structure determination using metagenome sequence data. Science 355, 294-298 (2017).
Crooks, G. E., Hon, G., Chandonia, J. M. & Brenner, S. E. WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190 (2004).
Bickford, J. S. & Nick, H. S. Conservation of the PTEN catalytic motif in the bacterial undecaprenyl pyrophosphate phosphatase, BacA/UppP. Microbiology 159, 2444-2455 (2013).