Insight into the structure of an endopolygalacturonase from the phytopathogen Burkholderia cepacia: a biochemical and computational study

Biochimie
Claudia MassaClaudio Anselmi

Abstract

We have recently investigated and characterized the mode of action of BcPeh28A, an endopolygalacturonase (endoPG) from the phytopathogen Burkholderia cepacia. EndoPGs belong to glycoside hydrolase family 28 and are responsible for the hydrolysis of the non-esterified regions of pectins. Here we report a 3-D structural model of BcPeh28A by combining mass spectrometry (MS) analysis, aimed at disulphide bridges mapping, and computational modelling tools. MS analyses have revealed the complete pattern of disulphide bridges in BcPeh28A, pointing out the presence of three disulphide bonds, defined as Cys3-25, Cys216-244 and Cys309-421. A 3-D model of BcPeh28A was generated by computational methods based on profile-profile sequence alignments and fold recognition algorithms. The final model exhibits a right-handed β-helix fold with eleven β-helical coils and includes the disulphide bonds as additional spatial restraints. Molecular dynamics simulations have been performed to test the conformational stability of the model. Finally, the structural analysis of the BcPeh28A model allows defining the architecture and the amino acid topology of the subsites involved in the catalysis and in the substrate binding specificity.

References

Sep 2, 1998·Journal of Structural Biology·S HeffronF Jurnak
Sep 2, 1998·Journal of Structural Biology·J JenkinsR Pickersgill
Sep 12, 1998·The Journal of Biological Chemistry·R PickersgillJ Jenkins
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Sep 28, 2000·Current Opinion in Chemical Biology·C S Rye, S G Withers
Nov 1, 2001·Proceedings of the National Academy of Sciences of the United States of America·L FedericiD Tsernoglou
Dec 26, 2001·Proceedings of the National Academy of Sciences of the United States of America·P BradleyB Berger
Nov 19, 2003·FEBS Letters·Gertie van PouderoyenBauke W Dijkstra
Feb 12, 2004·Biochimica Et Biophysica Acta·Renato D'OvidioDaniela Bellincampi
Feb 12, 2004·Biochimica Et Biophysica Acta·Jens Frisbaek SørensenNathalie Juge
Jun 28, 2005·Nucleic Acids Research·Lukasz JaroszewskiAdam Godzik
Jun 28, 2005·Nucleic Acids Research·John C GordonAlexey Onufriev
Jan 13, 2006·Trends in Plant Science·Luca FedericiFelice Cervone
Apr 6, 2006·Bioinformatics·Christian X Weichenberger, Manfred J Sippl
May 23, 2007·Nucleic Acids Research·Markus Wiederstein, Manfred J Sippl
Jul 14, 2007·The Biochemical Journal·Claudia MassaCristiana Campa
May 30, 2009·Journal of Computational Chemistry·Zhongqiao Hu, Jianwen Jiang

❮ Previous
Next ❯

Citations

Oct 22, 2013·Fungal Genetics and Biology : FG & B·Heliana Argôlo Santos CarvalhoFabienne Micheli

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cajal Bodies & Gems

Cajal bodies or coiled bodies are dense foci of coilin protein. Gemini of Cajal bodies, or gems, are microscopically similar to Cajal bodies. It is believed that Cajal bodies play important roles in RNA processing while gems assist the Cajal bodies. Find the latest research on Cajal bodies and gems here.

Cardiac Glycosides

Cardiac glycosides are a diverse family of naturally derived compounds that bind to and inhibit na+/k+-atpase. Discover the latest research on cardiac glycosides heres.

Related Papers

Nucleic Acids Research
E QuevillonR Lopez
Current Opinion in Structural Biology
C B Burge, S Karlin
© 2021 Meta ULC. All rights reserved