New structures of Class II Fructose-1,6-Bisphosphatase from Francisella tularensis provide a framework for a novel catalytic mechanism for the entire class

Selezneva, Anna I.; Harding, Luke N. M.; Gutka, Hiten J.; Movahedzadeh, Farahnaz; Abad-Zapatero, Celerino

doi:10.1371/journal.pone.0274723

New structures of Class II Fructose-1,6-Bisphosphatase from Francisella tularensis provide a framework for a novel catalytic mechanism for the entire class

Journal Article · Fri Jun 23 00:00:00 EDT 2023 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0274723· OSTI ID:2423540

Selezneva, Anna I. ^[1]; Harding, Luke N. M. ^[1]; Gutka, Hiten J. ^[2]; Movahedzadeh, Farahnaz ^[1]; Abad-Zapatero, Celerino ^[1]

University of Illinois, Chicago, IL (United States)
University of Illinois, Chicago, IL (United States); Bristol-Myers Squibb, Summit, NJ (United States)

Class II Fructose-1,6-bisphosphatases (FBPaseII) (EC: 3.1.3.11) are highly conserved essential enzymes in the gluconeogenic pathway of microorganisms. Previous crystallographic studies of FBPasesII provided insights into various inactivated states of the enzyme in different species. Presented here is the first crystal structure of FBPaseII in an active state, solved for the enzyme from Francisella tularensis (FtFBPaseII), containing native metal cofactor Mn²⁺ and complexed with catalytic product fructose-6-phosphate (F6P). Another crystal structure of the same enzyme complex is presented in the inactivated state due to the structural changes introduced by crystal packing. Analysis of the interatomic distances among the substrate, product, and divalent metal cations in the catalytic centers of the enzyme led to a revision of the catalytic mechanism suggested previously for class II FBPases. We propose that phosphate-1 is cleaved from the substrate fructose-1,6-bisphosphate (F1,6BP) by T89 in a proximal α-helix backbone (G88-T89-T90-I91-T92-S93-K94) in which the substrate transition state is stabilized by the positive dipole of the $$\langle$$-helix backbone. Once cleaved a water molecule found in the active site liberates the inorganic phosphate from T89 completing the catalytic mechanism. Additionally, a crystal structure of Mycobacterium tuberculosis FBPaseII (MtFBPaseII) containing a bound F1,6BP is presented to further support the substrate binding and novel catalytic mechanism suggested for this class of enzymes.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: Chicago Biomedical Consortium; Potts Memorial Foundation; USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 2423540

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 6 Vol. 18; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

References (23)

Data mining crystallization databases: Knowledge-based approaches to optimize protein crystal screens Kimber, Matthew S.; Vallee, François; Houston, Simon Proteins: Structure, Function, and Bioinformatics, Vol. 51, Issue 4 https://doi.org/10.1002/prot.10340	journal	May 2003
Enzymatic Characterization of Fructose 1,6-Bisphosphatase II from Francisella tularensis, an Essential Enzyme for Pathogenesis Gutka, Hiten J.; Wolf, Nina M.; Bondoc, Jasper Marc G. Applied Biochemistry and Biotechnology, Vol. 183, Issue 4 https://doi.org/10.1007/s12010-017-2512-6	journal	May 2017
A malachite green procedure for orthophosphate determination and its use in alkaline phosphatase-based enzyme immunoassay Baykov, A. A.; Evtushenko, O. A.; Avaeva, S. M. Analytical Biochemistry, Vol. 171, Issue 2 https://doi.org/10.1016/0003-2697(88)90484-8	journal	June 1988
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Study on the interaction between cyanobacteria FBP/SBPase and metal ions Sun, Yao; Liao, Xun; Li, Ding Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Vol. 89 https://doi.org/10.1016/j.saa.2011.12.014	journal	April 2012
The First Crystal Structure of the Novel Class of Fructose-1,6-Bisphosphatase Present in Thermophilic Archaea Nishimasu, Hiroshi; Fushinobu, Shinya; Shoun, Hirofumi Structure, Vol. 12, Issue 6 https://doi.org/10.1016/j.str.2004.03.026	journal	June 2004
Francisella tularensis travels a novel, twisted road within macrophages Santic, Marina; Molmeret, Maelle; Klose, Karl E. Trends in Microbiology, Vol. 14, Issue 1 https://doi.org/10.1016/j.tim.2005.11.008	journal	January 2006
Crystal Structures of Fructose 1,6-Bisphosphatase: Mechanism of Catalysis and Allosteric Inhibition Revealed in Product Complexes ^† ^, ^‡ Choe, Jun-Yong; Fromm, Herbert J.; Honzatko, Richard B. Biochemistry, Vol. 39, Issue 29 https://doi.org/10.1021/bi000574g	journal	July 2000
The α-helix dipole and the properties of proteins Hol, W. G. J.; van Duijnen, P. T.; Berendsen, H. J. C. Nature, Vol. 273, Issue 5662 https://doi.org/10.1038/273443a0	journal	June 1978
A Novel Candidate for the True Fructose-1,6-bisphosphatase in Archaea Rashid, Naeem; Imanaka, Hiroyuki; Kanai, Tamotsu Journal of Biological Chemistry, Vol. 277, Issue 34 https://doi.org/10.1074/jbc.M202868200	journal	August 2002
Structural and Biochemical Characterization of the Type II Fructose-1,6-bisphosphatase GlpX from Escherichia coli Brown, Greg; Singer, Alexander; Lunin, Vladimir V. Journal of Biological Chemistry, Vol. 284, Issue 6 https://doi.org/10.1074/jbc.M808186200	journal	February 2009
MOLREP an Automated Program for Molecular Replacement Vagin, A.; Teplyakov, A. Journal of Applied Crystallography, Vol. 30, Issue 6, p. 1022-1025 https://doi.org/10.1107/S0021889897006766	journal	December 1997
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
Presenting your structures: the CCP 4 mg molecular-graphics software McNicholas, S.; Potterton, E.; Wilson, K. S. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911007281	journal	March 2011
Structure of rabbit liver fructose 1,6-bisphosphatase at 2.3 Å resolution Weeks, Charles M.; Roszak, Aleksander W.; Erman, Mary Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 1 https://doi.org/10.1107/S0907444998008750	journal	January 1999
Structural and biochemical characterization of the class II fructose-1,6-bisphosphatase from Francisella tularensis Selezneva, Anna I.; Gutka, Hiten J.; Wolf, Nina M. Acta Crystallographica Section F Structural Biology Communications, Vol. 76, Issue 11 https://doi.org/10.1107/S2053230X20013370	journal	October 2020
Polder maps: improving OMIT maps by excluding bulk solvent Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W. Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 2, p. 148-157 https://doi.org/10.1107/S2059798316018210	journal	February 2017
Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition Wolf, Nina M.; Gutka, Hiten J.; Movahedzadeh, Farahnaz Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 4 https://doi.org/10.1107/S2059798318002838	journal	April 2018
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
Purification and Characterization of glpX-Encoded Fructose 1,6-Bisphosphatase, a New Enzyme of the Glycerol 3-Phosphate Regulon of Escherichia coli Donahue, J. L.; Bownas, J. L.; Niehaus, W. G. Journal of Bacteriology, Vol. 182, Issue 19 https://doi.org/10.1128/JB.182.19.5624-5627.2000	journal	October 2000
Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis Lassila, Jonathan K.; Zalatan, Jesse G.; Herschlag, Daniel Annual Review of Biochemistry, Vol. 80, Issue 1 https://doi.org/10.1146/annurev-biochem-060409-092741	journal	July 2011
Identification of Genes Contributing to the Virulence of Francisella tularensis SCHU S4 in a Mouse Intradermal Infection Model Kadzhaev, Konstantin; Zingmark, Carl; Golovliov, Igor PLoS ONE, Vol. 4, Issue 5 https://doi.org/10.1371/journal.pone.0005463	journal	May 2009

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
Biochemical cofactors
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Enzyme structure
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Phosphates
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New structures of Class II Fructose-1,6-Bisphosphatase from Francisella tularensis provide a framework for a novel catalytic mechanism for the entire class

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