A theoretical study on nitric oxide reductase activity in a ba 3-type heme-copper oxidase

Biochimica et Biophysica Acta - Bioenergetics

Volumn 1757, Issue 1, 2006, Pages 31-46

  Blomberg, L Mattias ^a   Blomberg, Margareta R A ^a   Siegbahn, Per E M ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

B3LYP; CcO; Cytochrome c oxidase; DFT; Electron transfer; Heme copper oxidase; Nitric oxide; Nitric oxide reductase; Nitrous oxide; NOR; Reduction

Indexed keywords

ANION; COPPER; FERROUS ION; HEME; HYDROXYL GROUP; NITRIC OXIDE; NITRIC OXIDE REDUCTASE; NITROUS OXIDE; OXIDOREDUCTASE; OXYGEN; WATER;

ARTICLE; CATALYSIS; CHEMICAL BINDING; CHEMICAL BOND; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; ELECTRON TRANSPORT; ENERGY TRANSFER; ENZYME ACTIVITY; PRIORITY JOURNAL; PROTON TRANSPORT; THEORETICAL STUDY;

ELECTRON TRANSPORT; HEME; IRON; MODELS, MOLECULAR; NITRIC OXIDE; OXIDATION-REDUCTION; OXIDOREDUCTASES; PROTONS; THERMUS THERMOPHILUS; WATER;

EID: 30944449027     PISSN: 00052728     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbabio.2005.11.004     Document Type: Article

References (30)

1. W.G. Zumft Nitric oxide reductases of prokaryotes with emphasis on the respiratory, heme-copper oxidase type J. Inorg. Biochem. 99 2005 194 215
2. M.R. Cheesman, W.G. Zumft, and A.J. Thomson The mcd and epr of the heme centers of nitric oxide reductase from Pseudomonas stutzeri: evidence that the enzyme is structurally related to the heme-copper oxidases Biochemistry 37 1998 3994 4000
3. J. Hendriks, A. Warne, U. Gohlke, T. Halita, C. Ludovici, M. Lübben, and M. Saraste The active site of the bacterial nitric oxide reductase is a dinuclear iron center Biochemistry 37 1998 13102 13109
4. A. Giuffré, G. Stubauer, P. Sarti, M. Brunori, W.G. Zumft, G. Buse, and T. Soulimane The heme-copper oxidases of Thermus thermophilus catalyze the reduction of nitric oxide: evolutionary implications Proc. Natl. Acad. Sci. U. S. A. 96 1999 14718 14723
5. 3 from Pseudomonas stutzeri displays nitric oxide reductase activity Eur. J. Biochem. 268 2001 6486 6490
6. 3 from Escherichia coli: the binding and turnover of nitric oxide Biochem. Biophys. Res. Commun. 296 2002 1272 1278
7. T. Fujiwara, and Y. Fukumori Cytochrome cb-type nitric oxide reductase with cytochrome c oxidase activity from Paracoccus denitrificans atcc 35512 J. Bacteriol. 178 1996 1866 1871
8. 3-cytochrome c oxidase from Thermus thermophilus EMBO J. 19 2000 1766 1776
9. A.D. Becke Density-functional thermochemistry: iii. The role of exact exchange J. Chem. Phys. 98 1993 5648 5652
10. C. Lee, W. Yang, and R.G. Parr Development of the colle-salvetti correlation-energy formula into a functional of the electron density Phys. Rev., B 37 1988 785 789
11. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, J.A. Montgomery Jr., R.E. Stratmann, J.C. Burant, S. Dapprich, J.M. Millan, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, J.L. Andres, M. Head-Gordon, E.S. Replogle, and J.A. Pople GAUSSIAN98 1998 Gaussian Inc Pittsburgh, PA
12. Schrödinger, Inc., Portland, Oregon, Jaguar 4.2 (2000).
13. L.M. Blomberg, M.R.A. Blomberg, and P.E.M. Siegbahn A theoretical study of myoglobin working as a nitric oxide scavenger J. Biol. Inorg. Chem. 9 2004 923 935
14. 2 by the cyclooxygenase active site in prostaglandin endoperoxide h synthase 1 J. Phys. Chem., B 107 2003 3297 3308
15. D.J. Tannor, B. Marten, R. Murphy, R.A. Friesner, D. Sitkoff, A. Nicholls, M. Ringnalda, W.A. Goddard III, and B. Honig Accurate first principles calculation of molecular charge distributions and solvation energies from ab initio quantum mechanics and continuum dielectric theory J. Am. Chem. Soc. 116 1994 11875 11882
16. M.R.A. Blomberg, P.E.M. Siegbahn, and G.T. Babcock Modeling electron transfer in biochemistry: a quantum chemical study of charge separation in Rhodobacter sphaeroides and photosystem ii J. Am. Chem. Soc. 120 1998 8812 8824
17. a values in cytochrome c oxidase J. Phys. Chem., B 109 2005 3616 3626
18. L.A. Curtiss, K. Raghavachari, R.C. Redfern, and J.A. Pople Assessment of gaussian-3 and density functional theories for a larger experimental test set J. Chem. Phys. 112 2000 7374 7383
19. P.E.M. Siegbahn, and M.R.A. Blomberg Density functional theory of biologically relevant metal centers Annu. Rev. Phys. Chem. 50 1999 221 249
20. P.E.M. Siegbahn, and M.R.A. Blomberg Transition-metal systems in biochemistry studied by high-accuracy quantum chemical methods Chem. Rev. 100 2000 421 437
21. M.R.A. Blomberg, and P.E.M. Siegbahn A quantum chemical approach to the study of reaction mechanisms of redox-active metalloenzymes J. Phys. Chem., B 105 2001 9375 9386
22. C.E. Cooper Nitric oxide and iron proteins Biochim. Biophys. Acta 1411 1999 290 309
23. 3 Biochemistry 40 2001 7806 7811
24. 2, no and co to heme proteins J. Inorg. Biochem. 99 2005 949 958
25. V. Shafirovich, and S.V. Lymar Nitroxyl and its anion in aqueous solutions: spin states, protic equilibria, and reactivities toward oxygen and nitric oxide Proc. Natl. Acad. Sci. U. S. A. 99 2002 7340 7345
26. 3 oxidase from Thermus thermophilus Biochemistry 38 1999 9648 9658
27. P. Moënne-Loccoz, O.-M.H. Richter, H.-W. Huang, I.M. Wasser, R.A. Ghiladi, K.D. Karlin, and S. de Vries Nitric oxide reductase from Paracoccus denitrificans contains an oxo-bridged heme/non-heme diiron center J. Am. Chem. Soc. 122 2000 9344 9345
28. P.E.M. Siegbahn, M.R.A. Blomberg, and L.M. Blomberg Theoretical study of the energetics of proton pumping and oxygen reduction in cytochrome oxidase J. Phys. Chem., B 107 2003 10946 10955
29. nor) from Fusarium oxysporum J. Inorg. Biochem. 99 2005 185 193
30. M.A. Vincent, I.H. Hillier, and J. Ge How is nn bond formation facilitated by p450 reductase? A DFT study Chem. Phys. Lett. 407 2005 333 336