Elucidations of the catalytic cycle of NADH-cytochrome b5 reductase by X-ray crystallography: New insights into regulation of efficient electron transfer

Journal of Molecular Biology

Volumn 425, Issue 22, 2013, Pages 4295-4306

  Yamada, Mitsugu ^a   Tamada, Taro ^a   Takeda, Kazuki ^b   Matsumoto, Fumiko ^a   Ohno, Hiraku ^b   Kosugi, Masayuki ^b   Takaba, Kiyofumi ^b   Shoyama, Yoshinari ^a   Kimura, Shigenobu ^c   Kuroki, Ryota ^a   Miki, Kunio ^b  

^a JAPAN ATOMIC ENERGY AGENCY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c IBARAKI UNIVERSITY   (Japan)

Author keywords

crystal structure; electron transfer; oxidoreductase; reaction intermediate

Indexed keywords

CYTOCHROME B5 REDUCTASE; FLAVINE ADENINE NUCLEOTIDE; HYDROGEN; NICOTINAMIDE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE;

ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; ELECTRON TRANSPORT; HYDROGEN BOND; NONHUMAN; OXIDATION; PRIORITY JOURNAL; PROTEIN DOMAIN; X RAY CRYSTALLOGRAPHY;

SUS;

EID: 84886717602     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.06.010     Document Type: Article

References (41)

1. D.F. Becker, W. Zhu, and M.A. Moxley Flavin redox switching of protein functions Antioxid Redox Signaling 14 2011 1079 1091
2. T. Senda, M. Senda, S. Kimura, and T. Ishida Redox control of protein conformation in flavoproteins Antioxid Redox Signaling 11 2009 1741 1766
3. B.W. Lennon, C.H. Williams, and M.K. Ludwig Crystal structure of reduced thioredoxin reductase from Escherichia coli: structural flexibility in the isoalloxazine ring of the flavin adenine dinucleotide cofactor Protein Sci 8 1999 2366 2379
4. T.N. Gustafsson, T. Sandalova, J. Lu, A. Holmgren, and G. Schneider High-resolution structures of oxidized and reduced thioredoxin reductase from Helicobacter pylori Acta Crystallogr Sect D Biol Crystallogr 63 2007 833 843
5. M. Senda, S. Kishigami, S. Kimura, M. Fukuda, T. Ishida, and T. Senda Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and rieske-type [2Fe-2S] ferredoxin J Mol Biol 373 2007 382 400
6. 5 reductase containing both the catalytic site and an additional hydrophobic membrane-binding segment J Biol Chem 248 1973 793 799
7. T. Okayasu, M. Nagao, T. Ishibashi, and Y. Imai Purification and partial characterization of linoleoyl-CoA desaturase from rat liver microsomes Arch Biochem Biophys 206 1981 21 28
8. 5 reductase Biochemistry 23 1984 1418 1425
9. 5 in fatty acid desaturation by rat liver microsomes J Biochem 69 1971 155 167
10. 5-dependent microsomal fatty acid elongation and identification of product J Biol Chem 255 1980 11357 11364
11. V.V. Reddy, D. Kupfer, and E. Capsi Mechanism of C-5 double bond introduction in the biosynthesis of cholesterol by rat liver microsomes J Biol Chem 252 1977 2797 2801
12. 5 in heptatic microsomal mixed-function oxidation reactions Arch Biochem Biophys 143 1971 66 79
13. D.E. Hultquist, and P.G. Passon Catalysis of methanoglobin reduction by erythrocyte cytochrome B5 and cytochrome B5 reductase Nat New Biol 229 1971 252 254
14. + reductase: structure-function relationship as studied by site-directed mutagenesis and X-ray crystallography Biochemistry 34 1995 8371 8379
15. + reductase from nonphotosynthetic tissues Biochemistry 40 2001 14501 14508
16. 5 reductase at 1.56 Å resolution Acta Crystallogr Sect F Struct Biol Cryst Commun 63 2007 274 279
17. 5 reductase Acta Crystallogr Sect D Biol Crystallogr 60 2004 1929 1934
18. 5 reductase from pig liver microsomes J Biol Chem 262 1987 11801 11802
19. 5 reductase from pig liver at 2.4 Å resolution Biochemistry 34 1995 2763 2767
20. 5 reductase and the other flavin-dependent reductases FEBS Lett 361 1995 97 100
21. 5 reductase and the other flavin-dependent reductases: pyridine nucleotide-binding and interaction with an electron-transfer partner Proteins 26 1996 32 41
22. 5 reductase are now consistent Biochemistry 40 2001 13574 13582
23. + reductase: prototype for a structurally novel flavoenzyme family Science 251 1991 60 65
24. + reductase Nat Struct Biol 8 2001 117 121
25. C.C. Correll, M.L. Ludwig, C.M. Bruns, and P.A. Karplus Structural prototypes for an extended family of flavoprotein reductases: comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin Protein Sci 2 1993 2112 2133
26. C.C. Correll, C.J. Batie, D.P. Ballow, and M.L. Ludwig Phthalate dioxygenase reductase: a modular structure for electron transfer from pyridine nucleotides to [2Fe-2S] Science 258 1992 1604 1610
27. M. Ingelman, V. Bianchi, and H. Eklund The three-dimensional structure of flavodoxin reductase from Escherichia coli at 1.7 Å resolution J Mol Biol 268 1997 147 157
28. M. Wang, D.L. Roberts, R. Paschke, T.M. Shea, B.S.S. Masters, and J.J.P. Kim Three-dimensional structure of NADPH-cytochrome P450 reductase: prototype for FMN- and FAD-containing enzymes Proc Natl Acad Sci USA 94 1997 8411 8416
29. G. Lu, W.H. Campbell, G. Schneider, and Y. Lindqvist Crystal structure of the FAD-containing fragment of corn nitrate reductase at 2.5 Å resolution: relationship to other flavoprotein reductases Structure 2 1994 809 821
30. 5 reductase catalytic domain on protein stability and catalysis J Biochem 130 2001 481 490
31. 5 reductase Arch Biochem Biophys 389 2001 223 233
32. 5 reductase in catalysis and control of the rate-limiting step in electron transfer J Biol Chem 278 2003 3580 3589
33. 5 Biochemistry 16 1977 2725 2730
34. 5 reductase solubilized domain Biochim Biophys Acta 1430 1999 290 301
35. + reductase revealed by protein engineering and crystallographic studies Nat Struct Biol 6 1999 847 853
36. Y.J. Zheng, and R.L. Ornstein A theoretical study of the structure of flavin in different oxidation and protonation states J Am Chem Soc 188 1996 9402 9408
37. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol 276 1997 307 326
38. G.M. Sheldrick, and T.R. Schneider SHELXL: high-resolution refinement Methods Enzymol 277 1997 319 343
39. D.E. McRee XtalView: a visual protein crystallographic software system for X11/XView J Mol Graphics 10 1992 44 46
40. P.D. Adams, R.W. Grosse-Kunstleve, L.W. Hung, T.R. Ioerger, A.J. McCoy, and N.W. Moriarty PHENIX: building new software for automated crystallographic structure determination Acta Crystallogr Sect D Biol Crystallogr 58 2002 1948 1954
41. P. Emsley, B. Lohkamp, W.G. Scott, and K. Cowtan Features and development of Coot Acta Crystallogr Sect D Biol Crystallogr 66 2010 486 501