500
T. Marinoet al.
25. Zheng X, Reddy SY, Bruice TC (2007) Mechanism of methanol oxidation by quinoprotein
methanol dehydrogenase. PNAS 104:745–749. https://doi.org/10.1073/pnas.0610126104
26. Reddy SY, Bruice TC (2004) Determination of enzyme mechanisms by molecular dynamics:
studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase. Protein
Sci 13:1965–1978 (2004). https://doi.org/10.1110/ps.04673404
27. Idupulapati NB, Mainardi DS (2009) THEOCHEM 901:72–80. https://doi.org/10.1016/j.
theochem.2009.01.004
28. McSkimming A, Cheisson T, Carroll PJ, Schelter EJ (2018) Functional synthetic model
for the lanthanide-dependent quinoid alcohol dehydrogenase active site. J Am Chem Soc
140:1223–1226. https://doi.org/10.1021/jacs.7b12318
29. Nakagawa T, Mitsui R, Tani A, Sasa K, Tashiro S, Iwama T, Hayakawa T, Kawai K (2012)
A catalytic role of XoxF1 as La3+-dependent methanol dehydrogenase in Methylobacterium
extorquens strain AM1. PLoS ONE 7:e50480. https://doi.org/10.1371/journal.pone.0050480
30. Chu F, Beck DAC, Lidstrom ME (2016) MxaY regulates the lanthanide-mediated methanol
dehydrogenase switch in Methylomicrobium buryatense. PeerJ 4:e2435. https://doi.org/10.
7717/peerj.2435
31. Skovran E, Martinez-Gomez NC (2015) Just add lanthanides. Science 348:862–863. https://
doi.org/10.1126/science.aaa9091
32. Blomberg RMA, Borowski T, Himo F, Liao R-Z, Siegbahn PEM (2014) Quantum chemical
studies of mechanisms for metalloenzymes. Chem Rev 114:3601–3658, and references therein.
https://doi.org/10.1021/cr400388t
33. Piazzetta P, Marino T, Russo N (2014) Promiscuous ability of human carbonic anhydrase:
QM and QM/MM Investigation of carbon dioxide and carbodiimide hydration. Inorg Chem
53:3488–3493. https://doi.org/10.1021/ic402932y
34. Amata O, Marino T, Russo N (2011) Catalytic activity of a ζ-class zinc and cadmium containing
carbonic anhydrase. Compared work mechanisms. Phys Chem Chem Phys 13:3468–3477.
https://doi.org/10.1039/C0CP01053G
35. Liao R-Z, Yu G, Himo F (2010) Mechanism of tungsten-dependent acetylene hydratase
from quantum chemical calculations. PNAS 107:22523–22527. https://doi.org/10.1073/pnas.
1014060108
36. Ramos MJ, Fernandes PA (2008) Computational enzymatic catalysis. Acc Chem Res
41:689–698. https://doi.org/10.1021/ar7001045
37. Marino T, Russo N, Toscano M (2012) Catalytic mechanism of the arylsulfatase promiscuous
enzyme from pseudomonas aeruginosa. Chem Eur J 19:2185–2192. https://doi.org/10.1002/
chem.201201943
38. Gaussian 09, Revision D.01, Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA,
Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M,
Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M,
Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven
T, Montgomery Jr JA, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN,
Staroverov VN, Keith T, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC,
Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken
V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, R. Cammi R,
Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P,
Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox
DJ (2013) Gaussian, Inc., Wallingford, CT
39. Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula
into a functional of the electron density. Phys Rev B 37:785–789. https://doi.org/10.1103/
PhysRevB.37.785
40. Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem
Phys 98:5648–5652. https://doi.org/10.1063/1.464913
41. Andrae D, Haußermann H, Dolg M, Stoll H, Preuß H (1990) Energy-adjustedab initio pseudopotentials for the second and third row transition elements. Theor Chim Acta 77:123–141.
https://doi.org/10.1007/BF01114537
T. Marinoet al.
25. Zheng X, Reddy SY, Bruice TC (2007) Mechanism of methanol oxidation by quinoprotein
methanol dehydrogenase. PNAS 104:745–749. https://doi.org/10.1073/pnas.0610126104
26. Reddy SY, Bruice TC (2004) Determination of enzyme mechanisms by molecular dynamics:
studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase. Protein
Sci 13:1965–1978 (2004). https://doi.org/10.1110/ps.04673404
27. Idupulapati NB, Mainardi DS (2009) THEOCHEM 901:72–80. https://doi.org/10.1016/j.
theochem.2009.01.004
28. McSkimming A, Cheisson T, Carroll PJ, Schelter EJ (2018) Functional synthetic model
for the lanthanide-dependent quinoid alcohol dehydrogenase active site. J Am Chem Soc
140:1223–1226. https://doi.org/10.1021/jacs.7b12318
29. Nakagawa T, Mitsui R, Tani A, Sasa K, Tashiro S, Iwama T, Hayakawa T, Kawai K (2012)
A catalytic role of XoxF1 as La3+-dependent methanol dehydrogenase in Methylobacterium
extorquens strain AM1. PLoS ONE 7:e50480. https://doi.org/10.1371/journal.pone.0050480
30. Chu F, Beck DAC, Lidstrom ME (2016) MxaY regulates the lanthanide-mediated methanol
dehydrogenase switch in Methylomicrobium buryatense. PeerJ 4:e2435. https://doi.org/10.
7717/peerj.2435
31. Skovran E, Martinez-Gomez NC (2015) Just add lanthanides. Science 348:862–863. https://
doi.org/10.1126/science.aaa9091
32. Blomberg RMA, Borowski T, Himo F, Liao R-Z, Siegbahn PEM (2014) Quantum chemical
studies of mechanisms for metalloenzymes. Chem Rev 114:3601–3658, and references therein.
https://doi.org/10.1021/cr400388t
33. Piazzetta P, Marino T, Russo N (2014) Promiscuous ability of human carbonic anhydrase:
QM and QM/MM Investigation of carbon dioxide and carbodiimide hydration. Inorg Chem
53:3488–3493. https://doi.org/10.1021/ic402932y
34. Amata O, Marino T, Russo N (2011) Catalytic activity of a ζ-class zinc and cadmium containing
carbonic anhydrase. Compared work mechanisms. Phys Chem Chem Phys 13:3468–3477.
https://doi.org/10.1039/C0CP01053G
35. Liao R-Z, Yu G, Himo F (2010) Mechanism of tungsten-dependent acetylene hydratase
from quantum chemical calculations. PNAS 107:22523–22527. https://doi.org/10.1073/pnas.
1014060108
36. Ramos MJ, Fernandes PA (2008) Computational enzymatic catalysis. Acc Chem Res
41:689–698. https://doi.org/10.1021/ar7001045
37. Marino T, Russo N, Toscano M (2012) Catalytic mechanism of the arylsulfatase promiscuous
enzyme from pseudomonas aeruginosa. Chem Eur J 19:2185–2192. https://doi.org/10.1002/
chem.201201943
38. Gaussian 09, Revision D.01, Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA,
Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M,
Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M,
Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven
T, Montgomery Jr JA, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN,
Staroverov VN, Keith T, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC,
Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken
V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, R. Cammi R,
Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P,
Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox
DJ (2013) Gaussian, Inc., Wallingford, CT
39. Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula
into a functional of the electron density. Phys Rev B 37:785–789. https://doi.org/10.1103/
PhysRevB.37.785
40. Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem
Phys 98:5648–5652. https://doi.org/10.1063/1.464913
41. Andrae D, Haußermann H, Dolg M, Stoll H, Preuß H (1990) Energy-adjustedab initio pseudopotentials for the second and third row transition elements. Theor Chim Acta 77:123–141.
https://doi.org/10.1007/BF01114537