Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A

Nature Structural Biology

Volumn 10, Issue 9, 2003, Pages 681-687

  Bertero, Michela G ^a   Rothery, Richard A ^b   Palak, Monica ^b   Hou, Cynthia ^a   Lim, Daniel ^a   Blasco, Francis ^c   Weiner, Joel H ^b   Strynadka, Natalie C J ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF ALBERTA   (Canada)

^c CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

NITRATE REDUCTASE;

ANAEROBIC METABOLISM; ARTICLE; ELECTRON TRANSPORT; ENZYME STRUCTURE; ENZYME SUBSTRATE; ESCHERICHIA COLI; NONHUMAN; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; PROTEIN TRANSPORT; RESPIRATORY CHAIN; STRUCTURE ANALYSIS; SYNTHESIS;

CATALYSIS; CELL MEMBRANE; CRYSTALLOGRAPHY, X-RAY; CYTOPLASM; ELECTRON TRANSPORT; ELECTRONS; ESCHERICHIA COLI; MODELS, BIOLOGICAL; MODELS, MOLECULAR; NITRATE REDUCTASE; NITRATE REDUCTASES; OXIDATION-REDUCTION; PROTEIN STRUCTURE, TERTIARY; PROTONS;

ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0041318860     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb969     Document Type: Article

References (37)

1. Blasco, F. et al. The coordination and function of the redox centres of the membrane-bound nitrate reductases. Cell. Mol. Life Sci. 58, 179-193 (2001).
2. Rothery, R.A., Blasco, F., Magalon, A. & Weiner, J.H. The diheme cytochrome b subunit (Narl) of Escherichia coli nitrate reductase A (NarGHI): structure, function, and interaction with quinols. J. Mol. Microbiol. Biotechnol. 3, 273-283 (2001).
3. Mitchell, P. Possible molecular mechanisms of the protonmotive function of cytochrome systems. J. Theor. Biol. 62, 327-367 (1976).
4. Jormakka, M., Tornroth, S., Byrne, B. & Iwata, S. Molecular basis of proton motive force generation: structure of formate dehydrogenase-N. Science 295, 1863-1868 (2002).
5. von Heijne, G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol. 225, 487-494 (1992).
6. Forget, P. The bacterial nitrate reductases. Solubilization, purification and properties of the enzyme A of Escherichia coli K12. Eur. J. Biochem. 42, 325-332 (1974).
7. Jones, R.W. & Garland, P.B. Sites and specificity of the reaction of bipyridylium compounds with anaerobic respiratory enzymes of Escherichia coli. Effects of permeability barriers imposed by the cytoplasmic membrane. Biochem. J. 164, 199-211 (1977).
8. Page, C.C., Moser, C.C., Chen, X. & Dutton, P.L. Natural engineering principles of electron tunnelling in biological oxidation-reduction. Nature 402, 47-52 (1999).
9. Lancaster, C.R., Kroger, A., Auer, M. & Michel, H. Structure of fumarate reductase from Wolinella succinogenes at 2.2 Å resolution. Nature 402, 377-385 (1999).
10. Xia, D. et al. Crystal structure of the cytochrome bcl complex from bovine heart mitochondria. Science 277, 60-66 (1997).
11. Berks, B.C., Ferguson, S.J., Moir, J.W. & Richardson, D.J. Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. Biochim. Biophys. Acta 1232, 97-173 (1995).
12. Schindelin, H., Kisker, C., Hilton, J., Rajagopalan, K.V. & Rees, D.C. Crystal structure of DMSO reductase: redox-linked changes in molybdopterin coordination. Science 272, 1615-1621 (1996).
13. Schneider, F. et al. Crystal structure of dimethyl sulfoxide reductase from Rhodobacter capsulatus at 1.88 Å resolution. J. Mol. Biol. 263, 53-69 (1996).
14. 4 cluster. Science 275, 1305-1308 (1997).
15. Czjzek, M. et al. Crystal structure of oxidized trimethylamine N-oxide reductase from Shewanella massilia at 2.5 Å resolution. J. Mol. Biol. 284, 435-447 (1998).
16. Dias, J.M. et al. Crystal structure of the first dissimilatory nitrate reductase at 1.9 Å solved by MAD methods. Struct. Fold. Des. 7, 65-79 (1999).
17. Blasco, F. et al. NarJ is a specific chaperone required for molybdenum cofactor assembly in nitrate reductase A of Escherichia coli. Mol. Microbiol. 28, 435-447 (1998).
18. Volbeda, A. et al. Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas. Nature 373, 580-587 (1995).
19. Peters, J.W., Lanzilotta, W.N., Lemon, B.J. & Seefeldt, L.C. X-ray crystal structure of the Fe-only hydrogenase (Cpl) from Clostridium pasteurianum to 1.8 Å resolution. Science 282, 1853-1858 (1998).
20. Magalon, A. et al. Molybdenum cofactor properties and [Fe-S] cluster coordination in Escherichia coli nitrate reductase A: investigation by site-directed mutagenesis of the conserved His-50 residue in the NarG subunit. Biochemistry 37, 7363-7370 (1998).
21. Rabenstein, D., Greenberg, M. & Saetre, R. Potentiometric and polarimetric studies of complexation of molybdenum(VI) and tungsten(VI) by aspartic acid and glutamic acid. Inorg. Chem. 16, 1241-1243 (1977).
22. Enemark, J. & Garner, C. The coordination chemistry and function of the molybdenum centres of the oxomolybdoenzymes. J. Biol. Inorg. Chem. 2, 817-822 (1997).
23. Berks, B.C. et al. Sequence analysis of subunits of the membrane-bound nitrate reductase from a denitrifying bacterium: the integral membrane subunit provides a prototype for the dihaem electron-carrying arm of a redox loop. Mol. Microbiol. 15, 319-331 (1995).
24. Sieker, L.C., Adman, E. & Jensen, L.H. Structure of the Fe-S complex in a bacterial ferredoxin. Nature 235, 40-42 (1972).
25. Stephens, P.J., Jollie, D.R. & Warshel, A. Protein control of redox potentials of iron-sulfur proteins. Chem. Rev. 96, 2491-2514 (1996).
26. Yankovskaya, V. et al. Architecture of succinate dehydrogenase and reactive oxygen species generation. Science 299, 700-704 (2003).
27. Zhao, Z., Rothery, R.A. & Weiner, J.H. Transient kinetic studies of heme reduction in Escherichia coli nitrate reductase A (NarGHI) by menaquinol. Biochemistry 42, 5403-5413 (2003).
28. Blasco, F. et al. Formation of active heterologous nitrate reductases between nitrate reductases A and Z of Escherichia coli. Mol. Microbiol. 6, 209-219 (1992).
29. Guigliarelli, B. et al. Complete coordination of the four Fe-S centers of the β subunit from Escherichia coli nitrate reductase. Physiological, biochemical, and EPR characterization of site-directed mutants lacking the highest or lowest potential [4Fe-4S] clusters. Biochemistry 35, 4828-4836 (1996).
30. Otwinowski, Z.M. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
31. Terwilliger, T. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. D 55, 849-861 (1999).
32. Brünger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
33. De La Fortelle, E.B., Gerard. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472-494 (1997).
34. McRee, D.E. XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156-165 (1999).
35. Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950 (1991).
36. Bacon, D. & Anderson, W. A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graph. 6, 219-220 (1988).
37. Honig, B. & Nicholls, A. Classical electrostatics in biology and chemistry. Science 268, 1144-1149 (1995).