Skip to main content
SpringerLink
Log in

Theoretical insights into the catalytic mechanism of β-hexosaminidase

  • Regular Article
  • Published:
Theoretical Chemistry Accounts Aims and scope Submit manuscript

Abstract

The enzyme (β-Hex) has a specific role in the degradation of a particular type of glycolipid, the GM2 ganglioside. This specificity is also manifested by its unusual mechanism of substrate-assisted catalysis, which is considered to be an alternative pathway for the breakage of glycosidic bonds. We have studied its catalytic mechanism using a small model of the enzyme: substrate Michaelis complex with DFT and MP2/MP3 methods. The results reflect the intrinsic chemical reactivity of the active site, decoupled from the long-range enzyme electrostatic field. The mechanism supports, and adds further atomic detail, on the earlier mechanistic suggestions based on experimental data. Moreover, we also have compared the geometry and full potential energy surface obtained with nine different exchange–correlation functionals. It was surprising that the B3LYP activation energies were lower than the ones from some of the hybrid meta functionals (known by their excellent performance on kinetics) by as much as 10 kcal/mol and lower than the MP2 energies by more than 12 kcal/mol. It is known that B3LYP underestimates barriers but underestimations of this extent are unusual and surprising. The effect of the theoretical method on the geometry, usually supposed to be less significant, had in some cases a relevant influence in the mechanism. Therefore, a more thoughtful choice should be made when choosing a methodology for geometry optimization.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  1. Wolfenden R, Lu XD, Young G (1998) Spontaneous hydrolysis of glycosides. J Am Chem Soc 120(27):6814–6815

    Article  CAS  Google Scholar 

  2. Zechel DL, Withers SG (2000) Glycosidase mechanisms: anatomy of a finely tuned catalyst. Acc Chem Res 33(1):11–18

    Article  CAS  Google Scholar 

  3. Mark BL et al (2001) Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase. J Biol Chem 276(13):10330–10337

    Article  CAS  Google Scholar 

  4. Lemieux MJ et al (2006) Crystallographic structure of human beta-hexosaminidase A: interpretation of Tay-Sachs mutations and loss of G(M2) ganglioside hydrolysis. J Mol Biol 359(4):913–929

    Article  CAS  Google Scholar 

  5. Proia RL, Soravia E (1987) Organization of the gene encoding the human beta-hexosaminidase alpha-chain. J Biol Chem 262(12):5677–5681

    CAS  Google Scholar 

  6. Korneluk RG et al (1986) Isolation of CDNA clones coding for the alpha-subunit of human beta-hexosaminidase—extensive homology between the alpha-subunits and beta-subunits and studies on Tay-Sachs disease. J Biol Chem 261(18):8407–8413

    CAS  Google Scholar 

  7. Sandhoff K, Wassle W (1971) Purification and characterisation of 2 forms of human N-acetyl-beta-D-hexosaminidase. Hoppe-Seylers Zeitschrift Fur Physiologische Chemie 352(8):1113–1119

    Google Scholar 

  8. Leopoldini M et al (2007) The role of quantum chemistry in the elucidation of the elementary mechanisms of catalytic processes: from atoms, to surfaces, to enzymes. Theor Chem Acc 117(5–6):765–779

    Article  CAS  Google Scholar 

  9. Himo F (2006) Quantum chemical modeling of enzyme active sites and reaction mechanisms. Theor Chem Acc 116(1–3):232–240

    Article  CAS  Google Scholar 

  10. Sousa SF, Fernandes PA, Ramos MJ (2007) General performance of density functionals. J Phys Chem A 111(42):10439–10452

    Article  CAS  Google Scholar 

  11. Schwabe T, Grimme S (2007) Double-hybrid density functionals with long-range dispersion corrections: higher accuracy and extended applicability. Phys Chem Chem Phys 9(26):3397–3406

    Article  CAS  Google Scholar 

  12. Bras NF, Ramos MJ, Fernandes PA (2010) DFT studies on the beta-glycosidase catalytic mechanism: the deglycosylation step. J Mol Struct-Theochem 946(1–3):125–133

    Article  CAS  Google Scholar 

  13. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE et al (2004) Gaussian 03, Revision C. 02. Gaussian, Wallingford CT

    Google Scholar 

  14. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE et al (2009) Gaussian 09, Revision A. 02. Gaussian, Wallingford CT

    Google Scholar 

  15. Zhao Y, Truhlar DG (2008) Density functionals with broad applicability in chemistry. Acc Chem Res 41(2):157–167

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Requimte, Faculty of Sciences of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal

    Óscar Passos, Pedro Alexandrino Fernandes & Maria João Ramos

Authors
  1. Óscar Passos
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pedro Alexandrino Fernandes
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Maria João Ramos
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Maria João Ramos.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 16 kb)

Supplementary material 2 (TIFF 7208 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Passos, Ó., Fernandes, P.A. & Ramos, M.J. Theoretical insights into the catalytic mechanism of β-hexosaminidase. Theor Chem Acc 129, 119–129 (2011). https://doi.org/10.1007/s00214-011-0904-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00214-011-0904-1

Keywords

Search

Navigation