Computational study of the non-heme iron active site in superoxide reductase and its reaction with superoxide

Inorganic Chemistry

Volumn 42, Issue 2, 2003, Pages 446-456

  Silaghi Dumitrescu, Radu ^a,b   Silaghi Dumitrescu, Ioan ^b   Coulter, Eric D ^a   Kurtz Jr , Donald M ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b BABE BOLYAI UNIVERSITY   (Romania)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYLIC ACID; CYSTEINE; CYTOCHROME P450; GLUTAMIC ACID; HEME; HYDROGEN PEROXIDE; IMIDAZOLE; IRON; LIGAND; OXIDOREDUCTASE; PROTEIN; SUPEROXIDE; SUPEROXIDE REDUCTASE; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; CHEMICAL BOND; CHEMICAL REACTION; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; DIFFUSION; ENERGY; PROTON TRANSPORT; REDUCTION;

BINDING SITES; CYTOCHROME P-450 ENZYME SYSTEM; DATABASES, FACTUAL; DESULFOVIBRIO VULGARIS; FERROUS COMPOUNDS; IRON; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; OXIDATION-REDUCTION; OXIDOREDUCTASES; PYROCOCCUS FURIOSUS; WATER; X-RAY DIFFRACTION;

EID: 0037467749     PISSN: 00201669     EISSN: None     Source Type: Journal    
DOI: 10.1021/ic025684l     Document Type: Article

References (39)

1. Yeh, A.; Hu, Y.; Jenney, F. J.; Adams, M.; Rees, D. Biochemistry 2000, 39, 2499-2508.
2. Coelho. A.; Matias, P.; Fulop, V.; Thompson, A.; Gonzalez, A.; Carrondo, M. JBIC, J. Biol. Inorg. Chem. 1997, 2, 680-689.
3. Jenney, F. J.; Verhagen, M.; Cui, X.; Adams, M. Science 1999, 286, 306-308.
4. Coulter, E.; Kurtz. D. M., Jr. Arch. Biochem. Biophys. 2001, 394, 76-86.
5. Tavares, P.; Ravi, N.; Moura, J.; LeGall, J.; Huang, Y.; Crouse, B.; Johnson, M. K.; Huynh, B.; Moura, I. J. Biol. Chem. 1994, 269, 10504-10510.
6. Clay, M. D.; Jenney, F. E. J.; Noh, H. J.; Hagedoorn, P. L.; Adams, M. W. W.; Johnson, M. K. Biochemistry 2002, 41, 9833-9841.
7. Clay, M. D.; Jenney, F. J.; Hagedoorn, P.; George, G.; Adams, M.; Johnson, M. K. J. Am. Chem. Soc. 2002, 124, 788-805.
8. Coulter. E.; Emerson, J.; Kurtz, D. M., Jr.; Cabelli, D. J. Am. Chem. Soc. 2000, 122, 11555-11556.
9. Emerson, J.; Coulter, E.; Cabelli, D.; Phillips, R.; Kurtz, D. M., Jr. Biochemistry 2002, 41, 4348-4357.
10. Abreu, I.; Saraiva, L.; Soares, C.; Teixeira, M.; Cabelli, D. J. Biol. Chem. 2001, 276, 38995-39001.
11. Lombard, M.; Houee-Levin, C.; Touati, D.; Fontecave, M.; Niviere, V. Biochemistry 2001, 40, 5032-5050.
12. Niviere, V.; Lombard, M.; Fontecave, M.; Houee-Levin, C. FEBS Lett. 2001, 497, 171-173.
13. Loew, G. H.; Harris, D. L. Chem. Rev. 2000, 100, 407-419.
14. Siegbahn, P. E. M.; Blomberg, M. R. A. Annu. Rev. Phys. Chem. 1999, 50, 221-49.
15. Siegbahn, P. E. M.; Blomberg, M. R. A. Chem. Rev. 2000, 100, 421-437.
16. To adjust the sequence numbering in the crystal structures to the D. vulgaris SOR numbering used here, 1 should be added to the residue numbers in the D. desulfuricans SOR structure and 33 (for Glul4, Lysl5, Hisl6), 28 (for His41 and His47), or 5 (for His114) should be added to the residue numbers in the P. furiosus SOR structures.
17. (a) Spartan 5.0; Wavefunction, Inc.: Irvine, CA.
18. (b) Becke, A. D. Phys. Rev. 1988, A38, 3089.
19. (c) Perdew, J. P. Phys. Rev. 1986, B33, 8822.
20. HyperChem Molecular Modelling System, Release 4.5 SGI, Hypercube; Hypercube, Inc. Hyperchem Molecular Modelling System, Release 5.01 for Windows; Hypercube, Inc.
21. HyperChem Molecular Modelling System, Release 4.5 SGI, Hypercube; Hypercube, Inc. Hyperchem Molecular Modelling System, Release 5.01 for Windows; Hypercube, Inc.
22. His49 Nδ in the D. desulfuricans SOR crystal structure appears to be involved in an unusual hydrogen bond with a main-chain peptide NH, implying a deprotonated imidazole ligand. However, this interaction is not present in any of the P. furiosus SOR X-ray structures.
23. These steric constraints are imposed by interactions with conserved Trp122, Pro70, Leu118, and Ile77, as well as by interactions between the His I19 Cβ and His49 heterocycle, and between each of the adjacent histidine ring planes.
24. Calculated values of the S-Fe-NeHis49 and Cys116Cβ-S-Fe angles were independent of the geometrical constraints imposed on the dihedral angles, and similar to the values observed in the SOR crystal structures.
25. Adams, M. W. W.; Jenney, F. E.; Clay, M. D.; Johnson, M. K. JBIC, J Biol. Inorg. Chem. 2002, 7, 647-652.
26. Kurtz, D. M., Jr. Essays Biochem. 1999, 34, 85-100.
27. Allen, F. H.; Kennard, O. Chem. Des. Autom. News 1993. 1, 31-37.
28. Similar ZINDO/S-CI calculations were performed on S = 1/2 model 4 (low-spin end-on peroxo). Because results on models 4 and 6 were essentially identical (i.e., they both feature one single strong transition in the visible domain, arising from sulfur-to-iron charge transfer with some imidazole-to-iron contribution), only results on S = 1/2 model 6 are reported here.
29. Neese, F.; Zaleski, M.; Loeb, K.; Solomon, E. I. J. Am. Chem. Soc. 2000, 122, 11703-11724.
30. Sigfridsson, E.; Olsson, M. H. M.; Ryde, U. Inorg. Chem 2001, 40, 2509-2519.
31. The B3LYP study by Sigfridsson et al. yields an Fe-S bond length (2.34 Å) that is in good agreement with the 2.37-Å distance determined by EXAFS of P. furiosus SOR. The difference between the B3LYP results and our data (Fe-S 2.25 Å) is likely due to the hybrid (Hartree-Fock/DFT) character of the B3LYP functional. A Hartree-Fock/3-21G* geometry optimization on our model 1 (our unpublished results) yielded a longer Fe-S bond, 2.47 Å.
32. Indeed, there is no indication of C-H···S hydrogen bonds between histidines and cysteines in any protein. See: Baures, P. W.; Beatty, A. M.; Dhanasekaran, M.; Helfrich, B. A.; Perez-Segarra, W.; Desper, J. J. Am. Chem. Soc. 2002, 124, 11315-11323.
33. Girerd, J.; Banse, F.; Simaan, A. Struct. Bonding (Berlin) 2000, 97, 145-176.
34. Solomon, E. I.; Brunold, T. C.; Davis, M. I.; Kemsley, J. N.; Lee, S. K.; Lehnert, N.; Neese, N.; Skulan, A. J.; Yang, Y. S.; Zhou, Z. Chem. Rev. 2000, 100, 235-350.
35. Shearer, J.; Scarrow, R. C.; Kovacs, J. A. J. Am. Chem. Soc. 2002, 124, 11707-11717.
36. Sono, M.; Roach, M. P.; Coulter, E. D.; Dawson, J. H. Chem. Rev. 1996, 96, 2841-2887.
37. Harris, D. L.; Loew, G. H. J. Am. Chem. Soc. 1998, 120, 8941-8948.
38. Harris, D. L. J. Inorg. Biochem. 2002, 91, 568-585.
39. Ogliaro, F.; de Visser, S. P.; Cohen, S.; Sharma, P. K.; Shaik, S. J. Am. Chem. Soc. 2002, 124, 2806-2817.