From a generated PES, one can determine the relative energies of species involved, the sequence in which they occur, and the activation barrier(s) associated with individual steps or the overall mechanism. Furthermore, they can provide more insights than a simple indication of a path of sequential mechanistic structures and their energetic relationships. The investigation into the activation of O2 by alpha-ketoglutarate-dependent dioxygenase (AlkB) clearly shows the opportunity for spin inversion, where one can see that the lowest energy product may be formed via several possible routes. In the investigation of uroporphyrinogen decarboxylase III (UROD), the use of QM/MM methods allowed for the inclusion of the anisotropic protein environment providing greater insight into the rate-limiting barrier. Lastly, the mechanism of 6-phospho-α-glucosidase (GlvA) was discussed using different active site models. In particular, a continuum model PES was compared to the gas-phase PES. 1. Introduction For a chemical reaction, enzymatic or nonenzymatic, the reactants, intermediates, and products all exist on a multidimensional surface. With this surface, a reaction is perfectly described by the statistical average of all possible paths from reactants to products via all possible intermediates [1]. However, a system with N atoms would require computing a (3N-6)-dimensional surface. Hence, if X number of points are to be computed for each of the (3N-6) dimensions, then calculations must be done [1]. Thus, such an undertaking is usually only computationally feasible for chemical models that consist of a few atoms. In contrast, studies on enzymatic mechanisms often necessarily require large chemical models consisting of important active site functional groups and cofactors and the substrate. Indeed, the cluster-based approach for investigating biochemical reactions typically use chemical models containing 200 atoms or more [2]. Thus, for such systems, it is impossible to determine the complete PES. Instead, a “slice” of the surface is typically constructed that involves only two coordinates, energy and reaction coordinate, and is commonly referred to as the PES [3]. The use and applicability of such “reduced-dimensionality” PESs reflects the fact that chemists and biochemists are usually only interested in key, mechanistically relevant structures including, for example, the (i) isolated reactants, (ii) reactive complex, (iii) transition structures (TS), (iv) intermediate(s), (v) product complex, and (vi) the separated products (Figure 1) [1]. It is noted that in general,
References
[1]
D. Young, Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems, Wiley-Interscience, New York, NY, USA, 2001.
[2]
P. E. M. Siegbahn and F. Himo, “Recent developments of the quantum chemical cluster approach for modeling enzyme reactions,” Journal of Biological Inorganic Chemistry, vol. 14, no. 5, pp. 643–651, 2009.
[3]
C. J. Cramer, Essentials of Computational Chemistry: Theories and Models, John Wiley & Sons, New York, NY, USA, 2002.
[4]
P. E. M. Siegbahn and T. Borowski, “Modeling enzymatic reactions involving transition metals,” Accounts of Chemical Research, vol. 39, no. 10, pp. 729–738, 2006.
[5]
F. Himo, “Quantum chemical modeling of enzyme active sites and reaction mechanisms,” Theoretical Chemistry Accounts, vol. 116, no. 1–3, pp. 232–240, 2006.
[6]
A. D. Becke, “A new mixing of Hartree-Fock and local density-functional theories,” The Journal of Chemical Physics, vol. 98, no. 2, pp. 1372–1377, 1993.
[7]
A. D. Becke, “Density-functional thermochemistry. III. The role of exact exchange,” The Journal of Chemical Physics, vol. 98, no. 7, pp. 5648–5652, 1993.
[8]
C. Lee, W. Yang, and R. G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Physical Review B, vol. 37, no. 2, pp. 785–789, 1988.
[9]
P. E. M. Siegbahn, “The performance of hybrid DFT for mechanisms involving transition metal complexes in enzymes,” Journal of Biological Inorganic Chemistry, vol. 11, no. 6, pp. 695–701, 2006.
[10]
B. Mennucci and J. Tomasi, “Continuum solvation models: a new approach to the problem of solute's charge distribution and cavity boundaries,” Journal of Chemical Physics, vol. 106, no. 12, pp. 5151–5158, 1997.
[11]
J. Tomasi, B. Mennucci, and E. Cancès, “The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level,” Journal of Molecular Structure: THEOCHEM, vol. 464, no. 1–3, pp. 211–226, 1999.
[12]
L. Hu, P. S？derhjelm, and U. Ryde, “On the convergence of QM/MM energies,” Journal of Chemical Theory and Computation, vol. 7, no. 3, pp. 761–777, 2011.
[13]
Y. Zhang, J. Kua, and J. A. McCammon, “Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies,” Journal of Physical Chemistry B, vol. 107, no. 18, pp. 4459–4463, 2003.
[14]
M. Kl？hn, S. Braun-Sand, E. Rosta, and A. Warshel, “On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions,” Journal of Physical Chemistry B, vol. 109, no. 32, pp. 15645–15650, 2005.
[15]
H. M. Senn and W. Thiel, “QM/MM methods for biomolecular systems,” Angewandte Chemie International Edition, vol. 48, no. 7, pp. 1198–1229, 2009.
[16]
J. Llano and J. W. Gauld, Mechanistics of Enzyme Catalysis: From Small to Large Active-Site Models, vol. 2, Wiley-VCH, Weinheim, Germany, 2010.
[17]
O. Acevedo and W. L. Jorgensen, “Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions,” Accounts of Chemical Research, vol. 43, no. 1, pp. 142–151, 2010.
[18]
M. Dal Peraro, P. Ruggerone, S. Raugei, F. L. Gervasio, and P. Carloni, “Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations,” Current Opinion in Structural Biology, vol. 17, no. 2, pp. 149–156, 2007.
[19]
Y. Hagiwara, M. J. Field, O. Nureki, and M. Tateno, “Editing Mechanism of Aminoacyl-tRNA synthetases operates by a hybrid ribozyme/protein catalyst,” Journal of the American Chemical Society, vol. 132, no. 8, pp. 2751–2758, 2010.
[20]
J. Blumberger, “Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment,” Physical Chemistry Chemical Physics, vol. 10, no. 37, pp. 5651–5667, 2008.
[21]
H. Liu, J. Llano, and J. W. Gauld, “A DFT study of nucleobase dealkylation by the DNA repair enzyme AlkB,” Journal of Physical Chemistry B, vol. 113, no. 14, pp. 4887–4898, 2009.
[22]
S. Shaik, H. Hirao, and D. Kumar, “Reactivity of high-valent iron-oxo species in enzymes and synthetic reagents: a tale of many states,” Accounts of Chemical Research, vol. 40, no. 7, pp. 532–542, 2007.
[23]
R. Poli and J. N. Harvey, “Spin forbidden chemical reactions of transition metal compounds. New ideas and new computational challenges,” Chemical Society Reviews, vol. 32, no. 1, pp. 1–8, 2003.
[24]
E. A. C. Bushnell, E. Erdtman, J. Llano, L. A. Eriksson, and J. W. Gauld, “The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase,” Journal of Computational Chemistry, vol. 32, no. 5, pp. 822–834, 2011.
[25]
P. J. Silva and M. J. Ramos, “Density-functional study of mechanisms for the cofactor-free decarboxylation performed by uroporphyrinogen III decarboxylase,” Journal of Physical Chemistry B, vol. 109, no. 38, pp. 18195–18200, 2005.
[26]
W. Huang, J. Llano, and J. W. Gauld, “Redox mechanism of glycosidic bond hydrolysis catalyzed by 6-phospho-α-glucosidase: a DFT study,” Journal of Physical Chemistry B, vol. 114, no. 34, pp. 11196–11206, 2010.
[27]
R. De Bont and N. van Larebeke, “Endogenous DNA damage in humans: a review of quantitative data,” Mutagenesis, vol. 19, no. 3, pp. 169–185, 2004.
[28]
Y. Wang, “Bulky DNA lesions induced by reactive oxygen species,” Chemical Research in Toxicology, vol. 21, no. 2, pp. 276–281, 2008.
[29]
J. S. Taylor, “Unraveling the molecular pathway from sunlight to skin cancer,” Accounts of Chemical Research, vol. 27, no. 3, pp. 76–82, 1994.
[30]
H. Kamiya, S. Iwai, and H. Kasai, “The (6-4) photoproduct of thymine-thymine induces targeted substitution mutations in mammalian cells,” Nucleic Acids Research, vol. 26, no. 11, pp. 2611–2617, 1998.
[31]
M. Lysetska, A. Knoll, D. Boehringer, T. Hey, G. Krauss, and G. Krausch, “UV light-damaged DNA and its interaction with human replication protein A: an atomic force microscopy study,” Nucleic Acids Research, vol. 30, no. 12, pp. 2686–2691, 2002.
[32]
W. L. Neeley and J. M. Essigmann, “Mechanisms of formation, genotoxicity, and mutation of guanine oxidation products,” Chemical Research in Toxicology, vol. 19, no. 4, pp. 491–505, 2006.
[33]
E. C. Friedberg, L. D. McDaniel, and R. A. Schultz, “The role of endogenous and exogenous DNA damage and mutagenesis,” Current Opinion in Genetics and Development, vol. 14, no. 1, pp. 5–10, 2004.
[34]
T. Lindahl, “Instability and decay of the primary structure of DNA,” Nature, vol. 362, no. 6422, pp. 709–715, 1993.
[35]
F. Drabl？s, E. Feyzi, P. A. Aas et al., “Alkylation damage in DNA and RNA—repair mechanisms and medical significance,” DNA Repair, vol. 3, no. 11, pp. 1389–1407, 2004.
[36]
Y. Mishina, E. M. Duguid, and C. He, “Direct reversal of DNA alkylation damage,” Chemical Reviews, vol. 106, no. 2, pp. 215–232, 2006.
[37]
B. Sedgwick, P. A. Bates, J. Paik, S. C. Jacobs, and T. Lindahl, “Repair of alkylated DNA: recent advances,” DNA Repair, vol. 6, no. 4, pp. 429–442, 2007.
[38]
T. Lindahl, B. Sedgwick, M. Sekiguchi, and Y. Nakabeppu, “Regulation and expression of the adaptive response to alkylating agents,” Annual Review of Biochemistry, vol. 57, pp. 133–157, 1988.
[39]
A. K. McCullough, M. L. Dodson, and R. S. Lloyd, “Initiation of base excision repair: glycosylase mechanisms and structures,” Annual Review of Biochemistry, vol. 68, pp. 255–285, 1999.
[40]
P. J. O'Brien and T. Ellenberger, “Human alkyladenine DNA glycosylase uses acid-base catalysis for selective excision of damaged purines,” Biochemistry, vol. 42, no. 42, pp. 12418–12429, 2003.
[41]
S. C. Trewick, T. F. Henshaw, R. P. Hausinger, T. Lindahl, and B. Sedgwick, “Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage,” Nature, vol. 419, no. 6903, pp. 174–178, 2002.
[42]
P. ？. Falnes, R. F. Johansen, and E. Seeberg, “AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli,” Nature, vol. 419, no. 6903, pp. 178–182, 2002.
[43]
T. Duncan, S. C. Trewick, P. Koivisto, P. A. Bates, T. Lindahl, and B. Sedgwick, “Reversal of DNA alkylation damage by two human dioxygenases,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 26, pp. 16660–16665, 2002.
[44]
L. Aravind and E. V. Koonin, “The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases,” Genome biology, vol. 2, no. 3, Article ID RESEARCH0007, 2001.
[45]
B. Yu, W. C. Edstrom, J. Benach et al., “Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB,” Nature, vol. 439, no. 7078, pp. 879–884, 2006.
[46]
Z. Zhang, J.-S. Ren, K. Harlos, C. H. McKinnon, I. J. Clifton, and C. J. Schofield, “Crystal structure of a clavaminate synthase-Fe(II)-2-oxoglutarate-substrate-NO complex: evidence for metal centred rearrangements,” FEBS Letters, vol. 517, no. 1–3, pp. 7–12, 2002.
[47]
R. Nakajima and I. Yamazaki, “The mechanism of oxyperoxidase formation from ferryl peroxidase and hydrogen peroxide,” Journal of Biological Chemistry, vol. 262, no. 6, pp. 2576–2581, 1987.
[48]
G. I. Berglund, G. H. Carlsson, A. T. Smith, H. Sz？ke, A. Henriksen, and J. Hajdu, “The catalytic pathway of horseradish peroxidase at high resolution,” Nature, vol. 417, no. 6887, pp. 463–468, 2002.
[49]
M. J. Frisch, G. W. Trucks, H. B. Schlegel, et al., Gaussian 03, Revision D.02, Gaussian, Inc., Wallingford, Conn, USA, 2004.
[50]
Jaguar, Schrodinger, L. L. C., Portland, Ore, USA, 5.5 edition, 1991–2003.
[51]
J. San Filippo Jr., L. J. Romano, C. I. Chern, and J. S. Valentine, “Cleavage of esters by superoxide,” Journal of Organic Chemistry, vol. 41, no. 3, pp. 586–588, 1976.
[52]
J. San Filippo Jr., C. I. Chern, and J. S. Valentine, “Oxidative cleavage of α-keto, α-hydroxy, and α-halo ketones, esters, and carboxylic acids by superoxide,” Journal of Organic Chemistry, vol. 41, no. 6, pp. 1077–1078, 1976.
[53]
Y. M. Chiou and L. Que, “Models for α-keto acid-dependent non-heme iron enzymes: structures and reactivity of [ CL(O2CCOPh)](ClO4) complexes,” Journal of the American Chemical Society, vol. 117, no. 14, pp. 3999–4013, 1995.
[54]
M. P. Mehn, K. Fujisawa, E. L. Hegg, and L. Que, “Oxygen activation by nonheme iron(II) complexes: α-keto carboxylate versus carboxylate,” Journal of the American Chemical Society, vol. 125, no. 26, pp. 7828–7842, 2003.
[55]
T. Borowski, A. Bassan, and P. E. M. Siegbahn, “Mechanism of dioxygen activation in 2-oxoglutarate-dependent enzymes: a hybrid DFT study,” Chemistry: A European Journal, vol. 10, no. 4, pp. 1031–1041, 2004.
[56]
T. Borowski, A. Bassan, and P. E. M. Siegbahn, “A hybrid density functional study of O-O bond cleavage and phenyl ring hydroxylation for a biomimetic non-heme iron complex,” Inorganic Chemistry, vol. 43, no. 10, pp. 3277–3291, 2004.
[57]
A. Bassan, T. Borowski, and P. E. M. Siegbahn, “Quantum chemical studies of dioxygen activation by mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad,” Dalton Transactions, no. 20, pp. 3153–3162, 2004.
[58]
T. Borowski, A. Bassan, and P. E. M. Siegbahn, “4-hydroxyphenylpyruvate dioxygenase: a hybrid density functional study of the catalytic reaction mechanism,” Biochemistry, vol. 43, no. 38, pp. 12331–12342, 2004.
[59]
G. F. Barnard and M. Akhtar, “Stereochemistry of porphyrinogen carboxy-lyase reaction in haem biosynthesis,” Journal of the Chemical Society, Chemical Communications, no. 13, pp. 494–496, 1975.
[60]
G. F. Barnard and M. Akhtar, “Stereochemical and mechanistic studies on the decarboxylation of uroporphyrinogen III in haem biosynthesis,” Journal of the Chemical Society, Perkin Transactions 1, pp. 2354–2360, 1979.
[61]
M. Akhtar, “The modification of acetate and propionate side chains during the biosynthesis of haem and chlorophylls: mechanistic and stereochemical studies,” Ciba Foundation symposium, vol. 180, pp. 131–152, 1994.
[62]
J. Fan, Q. Liu, Q. Hao, M. Teng, and L. Niu, “Crystal structure of uroporphyrinogen decarboxylase from Bacillus subtilis,” Journal of Bacteriology, vol. 189, no. 9, pp. 3573–3580, 2007.
[63]
I. U. Heinemann, M. Jahn, and D. Jahn, “The biochemistry of heme biosynthesis,” Archives of Biochemistry and Biophysics, vol. 474, no. 2, pp. 238–251, 2008.
[64]
B. M. Martins, B. Grimm, H. P. Mock, R. Huber, and A. Messerschmidt, “Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from Nicotiana tabacum: implications for the catalytic mechanism,” Journal of Biological Chemistry, vol. 276, no. 47, pp. 44108–44116, 2001.
[65]
H. P. Mock, L. Trainotti, E. Kruse, and B. Grimm, “Isolation, sequencing and expression of cDNA sequences encoding uroporphyrinogen decarboxylase from tobacco and barley,” Plant Molecular Biology, vol. 28, no. 2, pp. 245–256, 1995.
[66]
A. H. Jackson, H. A. Sancovich, A. M. Ferramola et al., “Macrocyclic intermediates in the biosynthesis of porphyrins,” Philosophical Transactions of the Royal Society of London. Series B, vol. 273, no. 924, pp. 191–206, 1976.
[67]
J. D. Phillips, F. G. Whitby, J. P. Kushner, and C. P. Hill, “Structural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase,” The EMBO Journal, vol. 22, no. 23, pp. 6225–6233, 2003.
[68]
G. Chaufan, M. C. Ríos de Molina, and L. C. San Martín de Viale, “How does hexachlorobenzene treatment affect liver uroporphyrinogen decarboxylase?” International Journal of Biochemistry and Cell Biology, vol. 33, no. 6, pp. 621–630, 2001.
[69]
C. A. Lewis and R. Wolfenden, “Uroporphyrinogen decarboxylation as a benchmark for the catalytic proficiency of enzymes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 45, pp. 17328–17333, 2008.
[70]
S. Billi de Catabbi, M. C. Ríos de Molina, and L. C. San Martín de Viale, “Studies on the active centre of rat liver porphyrinogen carboxylase in vivo effect of hexachlorobenzene,” International Journal of Biochemistry, vol. 23, no. 7-8, pp. 675–679, 1991.
[71]
K. M. Jones and P. M. Jordan, “Purification and properties of the uroporphyrinogen decarboxylase from Rhodobacter sphaeroides,” Biochemical Journal, vol. 293, no. 3, pp. 703–712, 1993.
[72]
M. Akhtar, New Comprehensive Biochemistry: Biosynthesis of Tetrapyrroles, vol. 19, Elsevier, London, UK, 1991.
[73]
M. J. Bearpark, F. Ogliaro, T. Vreven, et al., “CASSCF calculations for excited states of large molecules: choosing when to use the RASSCF, ONIOM and MMVB approximations,” in Computation in Modern Science and Engineering, Parts A and B, T. E. Simos and G. Maroulis, Eds., vol. 2, pp. 583–585, Amer Inst Physics, Melville, NY, USA, 2007.
[74]
S. Dapprich, I. Komáromi, K. S. Byun, K. Morokuma, and M. J. Frisch, “A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives,” Journal of Molecular Structure: THEOCHEM, vol. 461-462, pp. 1–21, 1999.
[75]
S. Humbel, S. Sieber, and K. Morokuma, “The IMOMO method: integration of different levels of molecular orbital approximations for geometry optimization of large systems: test for n-butane conformation and reaction: ,” Journal of Chemical Physics, vol. 105, no. 5, pp. 1959–1967, 1996.
[76]
F. Maseras and K. Morokuma, “IMOMM—a new integrated ab-initio plus molecular mechanics geometry optimization scheme of equilibrium structures and transition-states,” Journal of Computational Chemistry, vol. 16, no. 9, pp. 1170–1179, 1995.
[77]
K. Morokuma, D. G. Musaev, T. Vreven, H. Basch, M. Torrent, and D. V. Khoroshun, “Model studies of the structures, reactivities, and reaction mechanisms of metalloenzymes,” IBM Journal of Research and Development, vol. 45, no. 3-4, pp. 367–395, 2001.
[78]
M. Svensson, S. Humbel, R. D. J. Froese, T. Matsubara, S. Sieber, and K. Morokuma, “ONIOM: a multilayered integrated method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and oxidative addition,” Journal of Physical Chemistry, vol. 100, no. 50, pp. 19357–19363, 1996.
[79]
T. Vreven, K. S. Byun, I. Komáromi et al., “Combining quantum mechanics methods with molecular mechanics methods in ONIOM,” Journal of Chemical Theory and Computation, vol. 2, no. 3, pp. 815–826, 2006.
[80]
T. Vreven and K. Morokuma, “On the application of the IMOMO (integrated molecular orbital + molecular orbital) method,” Journal of Computational Chemistry, vol. 21, no. 16, pp. 1419–1432, 2000.
[81]
T. Vreven, K. Morokuma, O. Farkas, H. B. Schlegel, and M. J. Frisch, “Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints,” Journal of Computational Chemistry, vol. 24, no. 6, pp. 760–769, 2003.
[82]
D. A. Case, T. E. Cheatham, T. Darden et al., “The Amber biomolecular simulation programs,” Journal of Computational Chemistry, vol. 26, no. 16, pp. 1668–1688, 2005.
[83]
H. de Verneuil, S. Sassa, and A. Kappas, “Purification and properties of uroporphyrinogen decarboxylase from human erythrocytes. A single enzyme catalyzing the four sequential decarboxylations of uroporphyrinogens I and III,” Journal of Biological Chemistry, vol. 258, no. 4, pp. 2454–2460, 1983.
[84]
A. B. Juárez, C. Aldonatti, M. S. Vigna, and M. C. Ríos de Molina, “Studies on uroporphyrinogen decarboxylase from Chlorella kessleri (Trebouxiophyceae, Chlorophyta),” Canadian Journal of Microbiology, vol. 53, no. 2, pp. 303–312, 2007.
[85]
R. Wolfenden, X. Lu, and G. Young, “Spontaneous hydrolysis of glycosides,” Journal of the American Chemical Society, vol. 120, no. 27, pp. 6814–6815, 1998.
[86]
D. L. Zechel and S. G. Withers, “Glycosidase mechanisms: anatomy of a finely tuned catalyst,” Accounts of Chemical Research, vol. 33, no. 1, pp. 11–18, 2000.
[87]
J. M. Stubbs and D. Marx, “Glycosidic bond formation in aqueous solution: on the oxocarbenium intermediate,” Journal of the American Chemical Society, vol. 125, no. 36, pp. 10960–10962, 2003.
[88]
J. M. Stubbs and D. Marx, “Aspects of glycosidic bond formation in aqueous solution: chemical bonding and the role of water,” Chemistry: A European Journal, vol. 11, no. 9, pp. 2651–2659, 2005.
[89]
K. Das, D. Ray, N. R. Bandyopadhyay, T. Ghosh, A. K. Mohanty, and M. Misra, “A study of the mechanical, thermal and morphological properties of microcrystalline cellulose particles prepared from cotton slivers using different acid concentrations,” Cellulose, vol. 16, no. 5, pp. 783–793, 2009.
[90]
Q. P. Liu, G. Sulzenbacher, H. Yuan et al., “Bacterial glycosidases for the production of universal red blood cells,” Nature Biotechnology, vol. 25, no. 4, pp. 454–464, 2007.
[91]
B. Capon, “Mechanism in carbohydrate chemistry,” Chemical Reviews, vol. 69, no. 4, pp. 407–498, 1969.
[92]
B. Henrissat, “A classification of glycosyl hydrolases based on amino acid sequence similarities,” Biochemical Journal, vol. 280, no. 2, pp. 309–316, 1991.
[93]
J. D. McCarter and S. G. Withers, “Mechanisms of enzymatic glycoside hydrolysis,” Current Opinion in Structural Biology, vol. 4, no. 6, pp. 885–892, 1994.
[94]
B. Henrissat and G. Davies, “Structural and sequence-based classification of glycoside hydrolases,” Current Opinion in Structural Biology, vol. 7, no. 5, pp. 637–644, 1997.
[95]
M. L. Sinnott, “Catalytic mechanisms of enzymic glycosyl transfer,” Chemical Reviews, vol. 90, no. 7, pp. 1171–1202, 1990.
[96]
G. J. Davies, T. M. Gloster, and B. Henrissat, “Recent structural insights into the expanding world of carbohydrate-active enzymes,” Current Opinion in Structural Biology, vol. 15, no. 6, pp. 637–645, 2005.
[97]
B. P. Rempel and S. G. Withers, “Covalent inhibitors of glycosidases and their applications in biochemistry and biology,” Glycobiology, vol. 18, no. 8, pp. 570–586, 2008.
[98]
J. Thompson, C. R. Gentry-Weeks, N. Y. Nguyen, J. E. Folk, and S. A. Robrish, “Purification from Fusobacterium mortiferum ATCC 25557 of a 6-phosphoryl-O-α-D-glucopyranosyl:6-phosphoglucohydrolase that hydrolyzes maltose 6-phosphate and related phospho-α-D-glucosides,” Journal of Bacteriology, vol. 177, no. 9, pp. 2505–2512, 1995.
[99]
A. Varrot, V. L. Y. Yip, Y. Li et al., “NAD+ and metal-ion dependent hydrolysis by family 4 glycosidases: structural insight into specificity for phospho-β-D-glucosides,” Journal of Molecular Biology, vol. 346, no. 2, pp. 423–435, 2005.
[100]
J. Thompson, S. B. Ruvinov, D. I. Freedberg, and B. G. Hall, “Cellobiose-6-phosphate hydrolase (CelF) of Escherichia coli: characterization and assignment to the unusual family 4 of glycosylhydrolases,” Journal of Bacteriology, vol. 181, no. 23, pp. 7339–7345, 1999.
[101]
F. Kunst, N. Ogasawara, I. Moszer et al., “The complete genome sequence of the gram-positive bacterium Bacillus subtilis,” Nature, vol. 390, no. 6657, pp. 249–256, 1997.
[102]
J. Thompson, A. Pikis, S. B. Ruvinov, B. Henrissat, H. Yamamoto, and J. Sekiguchi, “The gene glvA of Bacillus subtilis 168 encodes a metal-requiring, NAD(H)-dependent 6-phospho-α-glucosidase. Assignment to family 4 of the glycosylhydrolase superfamily,” Journal of Biological Chemistry, vol. 273, no. 42, pp. 27347–27356, 1998.
[103]
B. G. Hall, A. Pikis, and J. Thompson, “Evolution and biochemistry of family 4 glycosidases: implications for assigning enzyme function in sequence annotations,” Molecular Biology and Evolution, vol. 26, no. 11, pp. 2487–2497, 2009.
[104]
B. I. Cantarel, P. M. Coutinho, C. Rancurel, T. Bernard, V. Lombard, and B. Henrissat, “The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics,” Nucleic Acids Research, vol. 37, no. 1, pp. D233–D238, 2009.
[105]
S. S. Rajan, X. Yang, F. Collart et al., “Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+-dependent phospho-α-glucosidase from Bacillus subtilis,” Structure, vol. 12, no. 9, pp. 1619–1629, 2004.
[106]
V. L. Y. Yip, J. Thompson, and S. G. Withers, “Mechanism of GlvA from Bacillus subtilis: a detailed kinetic analysis of a 6-phospho-α-glucosidase from glycoside hydrolase family 4,” Biochemistry, vol. 46, no. 34, pp. 9840–9852, 2007.
[107]
V. L.Y. Yip and S. G. Withers, “Family 4 glycosidases carry out efficient hydrolysis of thioglycosides by an α,β-elimination mechanism,” Angewandte Chemie International Edition, vol. 45, no. 37, pp. 6179–6182, 2006.
