Reduction of nitric oxide in bacterial nitric oxide reductase-a theoretical model study

Biochimica et Biophysica Acta - Bioenergetics

Volumn 1757, Issue 4, 2006, Pages 240-252

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

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

B3LYP; DFT; Heme copper oxidase; Nitric oxide; Nitric oxide reductase; Nitrous oxide; NOR

Indexed keywords

CYTOCHROME C OXIDASE; GLUTAMIC ACID; HEME; HISTIDINE; NITRIC OXIDE; NITRIC OXIDE REDUCTASE;

ARTICLE; CHEMICAL BOND; DENSITY FUNCTIONAL THEORY; ENZYME ACTIVE SITE; ENZYME DEGRADATION; ENZYME MECHANISM; ENZYME STRUCTURE; MOLECULAR MODEL; MOLECULAR STABILITY; PRIORITY JOURNAL; REDUCTION KINETICS; RESPIRATORY CHAIN; STRUCTURE ANALYSIS; THEORETICAL MODEL; THERMODYNAMICS;

BACTERIA; MODELS, MOLECULAR; MODELS, THEORETICAL; NITRIC OXIDE; OXIDATION-REDUCTION; OXIDOREDUCTASES;

BACTERIA (MICROORGANISMS);

EID: 33745203021     PISSN: 00052728     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbabio.2006.04.008     Document Type: Article

References (42)

1. Gardner A.M., Helmick R.A., and Gardner P.R. Flavorubredoxin, an inducible catalyst for nitric oxide reduction and detoxification in Escherichia coli. J. Biol. Chem. 277 (2002) 8172-8177
2. Nakahara K., Tanimoto T., Hatano K., Usuda K., and Shoun H. Cytochrome p-450 55a1 (p-450dnir) acts as nitric oxide reductase employing NADH as the direct electron donor. J. Biol. Chem. 268 (1993) 8350-8355
3. Cheesman M.R., Zumft W.G., and Thomson A.J. 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
4. Girsch P., and de Vries S. Purification and initial kinetic and spectroscopic characterization of no reductase from Paracoccus denitrificans. Biochim. Biophys. Acta 1318 (1997) 202-216
5. Grönberg K.L.C., Roldán M.D., Prior L., Butland G., Cheesman M.R., Richardson D.J., Spiro S., Thomson A.J., and Watmough N.J. A low-redox potential heme in the dinuclear center of bacterial nitric oxide reductase: implications for the evolution of energy-conserving heme-copper oxidases. Biochemistry 38 (1999) 13780-13786
6. Hendriks J., Gohlke U., and Saraste M. From no to oo: nitric oxide and dioxygen in bacterial respiration. J. Bioenerg. Biomembr. 30 (1998) 15-24
7. Sakurai N., and Sakurai T. Isolation and characterization of nitric oxide reductase from Paracoccus halodenitrificans. Biochemistry 36 (1997) 13809-13815
8. Hendriks J., Warne A., Gohlke U., Halita T., Ludovici C., Lübben M., and Saraste M. The active site of the bacterial nitric oxide reductase is a dinuclear iron center. Biochemistry 37 (1998) 13102-13109
9. Zumft W.G. Nitric oxide reductases of prokaryotes with emphasis on the respiratory heme- copper oxidase type. J. Inorg. Biochem. 99 (2005) 194-215
10. In: Kannt A., Michel H., Cheesman M.R., Thomson A.J., Dreusch A.B., Körner H., Zumft W.G., Canters G.W., and Vijgenboom E. (Eds). Biological electron transfer chains: genetics, composition and mode of operation (1998), Kluwer Academic Publishers, Dordrecht
11. Butland G., Spiro S., Watmough N.J., and Richardson D.J. Two conserved glutamates in the bacterial nitric oxide reductase are essential for activity but not assembly of the enzyme. J. Bacteriol. 183 (2001) 189-199
12. Hendriks J., Jasaitis A., Saraste M., and Verkhovsky M.I. Proton and electron pathways in the bacterial nitric oxide reductase. Biochemistry 41 (2002) 2331-2340
13. Moënne-Loccoz P., and de Vries S. Structural characterization of the catalytic high-spin heme b of nitric oxide reductase: a resonance raman study. J. Am. Chem. Soc. 120 (1998) 5147-5152
14. Que Jr. L. One motif-Many different reactions. Nature Struc. Biol. 7 (2000) 182-184
15. Que Jr. L., and Ho R.Y.N. Dioxygen activation by enzymes with mononuclear non-heme iron active sites. Chem. Rev. 96 (1996) 2607-2624
16. Silaghi-Dumitrescu R., Kurtz Jr. D.M., Ljungdahl L.G., and Lanzilotta W.N. X-ray crystal structures of Moorella thermoacetica fpra. novel diiron site structure and mechanistic insights into scavenging nitric oxide reductase. Biochemistry 44 (2005) 6492-6501
17. Silaghi-Dumitrescu R., Coulter E.D., Das A., Ljungdahl L.G., Jameson G.N.L., Huynh B.H., and Kurtz Jr. D.M. A flavodiiron protein and high molecular weight rubredoxin from moorellathermoacetica with nitric oxide reductase activity. Biochemistry 42 (2003) 2806-2815
18. Becke A.D. Density-functional thermochemistry. iii. The role of exact exchange. J. Chem. Phys. 98 (1993) 5648-5652
19. Lee C., Yang W., and Parr R.G. Development of the colle-salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B. 37 (1988) 785-789
20. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Montgomery J.J.A., Vreven T., Kudin K.N., Burant J.C., Millam J.M., Iyengar S.S., Tomasi J., Barone V., Mennucci B., Cossi M., Scalmani G., Rega N., Petersson G.A., Nakatsuji H., Hada M., Ehara K., Toyota M., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Klene M., Li X., Knox J.E., Hratchian H.P., Cross J.B., Adamo C., Jaramillo J., Gomperts R., Stratmann R.E., Yazyev O., Austin A.J., Cammi R., Pomelli C., Ochterski J.W., Ayala P.Y., Morokuma K., Voth G.A., Salvador P., Dannenberg J.J., Zakrzewski V.G., Dapprich S., Daniels A.D., Strain M.C., Farkas O., Malick D.K., Rabuck A.D., Raghavachari K., Foresman J.B., Ortiz J.V., Cui Q., Baboul A.G., Clifford S., Cioslowski J., Stefanov B.B., Liu G., Liashenko A., Piskorz P., Komaromi I., Martin R.L., Fox D.J., Keith T., Al-Laham M.A., Peng C.Y., Nanayakkara A., Challacombe M., Gill W., Johnson B., Chen W., Wong M.W., Gonzalez C., and Pople J.A. Gaussian 03, Revision B.03 (2003), Gaussian Inc., Pittsburgh, PA
21. Schrodinger, LLC, Portland, Oregon, Jaguar 5.5 (2003).
22. Blomberg L.M., Blomberg M.R.A., and Siegbahn P.E.M. A theoretical study of myoglobin working as a nitric oxide scavenger. J. Biol. Inorg. Chem. 9 (2004) 923-935
23. Blomberg L.M., Blomberg M.R.A., Siegbahn P.E.M., van der Donk W.A., and Tsai A.L. A quantum chemical study of the synthesis of prostaglandin g2 by the cyclooxygenase active site in prostaglandin endoperoxide h synthase 1. J. Phys. Chem., B. 107 (2003) 3297-3308
24. Tannor D.J., Marten B., Murphy R., Friesner R.A., Sitkoff D., Nicholls A., Ringnalda M., Goddard III W.A., and Honig B. 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
25. Blomberg M.R.A., Siegbahn P.E.M., and Babcock G.T. 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
26. a values in cytochrome c oxidase. J. Phys. Chem., B. 109 (2005) 3616-3626
27. Curtiss L.A., Raghavachari K., Redfern R.C., and Pople J.A. Assessment of gaussian-3 and density functional theories for a larger experimental test set. J. Chem. Phys. 112 (2000) 7374-7383
28. Siegbahn P.E.M., and Blomberg M.R.A. Density functional theory of biologically relevant metal centers. Annu. Rev. Phys. Chem. 50 (1999) 221-249
29. Siegbahn P.E.M., and Blomberg M.R.A. Transition-metal systems in biochemistry studied by high-accuracy quantum chemical methods. Chem. Rev. 100 (2000) 421-437
30. Blomberg M.R.A., and Siegbahn P.E.M. A quantum chemical approach to the study of reaction mechanisms of redox-active metalloenzymes. J. Phys. Chem., B. 105 (2001) 9375-9386
31. 3-type heme-copper oxidase. Biochim. Biophys. Acta 1757 (2006) 31-46
32. Pinakoulaki E., Gemeinhardt S., Saraste M., and Varotsis C. Nitric-oxide reductase structure and properties of the catalytic site from resonance raman scattering. J. Biol. Chem. 277 (2002) 23407-23413
33. 2, no and co to heme proteins. J. Inorg. Biochem. 99 (2005) 949-958
34. Kumita H., Matsuura K., Hino T., Takahashi S., Hori H., Fukumori Y., Morishima I., and Shiro Y. No reduction by nitric-oxide reductase from denitrifying bacterium Pseudomonas aeruginosa. J. Biol. Chem. 279 (2004) 55247-55254
35. Shafirovich V., and Lymar S.V. 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
36. IV{double bond, long}o core in tetrahydrobiopterin-dependent hydroxylases. Chem. Eur. J. 9 (2003) 4055-4067
37. Bassan A., Blomberg M.R.A., and Siegbahn P.E.M. Mechanism of dioxygen cleavage in tetrahydrobiopterin-dependent amino acid hydroxylases. Chem. Eur. J. 7 (2003) 106-115
38. 3 from Pseudomonas stutzeri displays nitric oxide reductase activity. Eur. J. Biochem. 268 (2001) 6486-6490
39. Moënne-Loccoz P., Richter O.-M.H., -w. Huang H., Wasser I.M., Ghiladi R.A., Karlin K.D., and de Vries S. Nitric oxide reductase from Paracoccus denitrificans contains an oxo-bridged heme/non-heme diiron center. J. Am. Chem. Soc. 122 (2000) 9344-9345
40. Field S.J., Prior L., Roldán M.D., Cheesman M.R., Thomson A.J., Spiro S., Butt J.N., Watmough N.J., and Richardson D.J. Spectral properties of bacterial nitric-oxide reductase. J. Biol. Chem. 277 (2002) 20146-20150
41. Price J.C., Barr E.W., Tirupati B., Bollinger Jr. J.M., and Krebs C. The first direct characterization of a high-valent iron intermediate in the reaction of an α-ketoglutarate-dependent dioxygenase: A high-spin fe(iv) complex in taurine/α-ketoglutarate dioxygenase (taud) from Escherichia coli. Biochemistry 42 (2003) 7497-7508
42. Riggs-Gelasco P.M., Price J.C., Guyer R.B., Brehm J.H., Barr E.W., Bollinger Jr. J.M., and Krebs C. Exafs spectroscopic evidence for an fe{double bond, long}o unit in the fe(iv) intermediate observed during oxygen activation by taurine:α-ketoglutarate dioxygenase. J. Am. Chem. Soc. 126 (2004) 8108-8109