Structure at 1.3 Å resolution of Rhodothermus marinus caa3 cytochrome c domain

Journal of Molecular Biology

Volumn 345, Issue 5, 2005, Pages 1047-1057

  Srinivasan, Vasundara ^a   Rajendran, Chitra ^a   Sousa, Filipa L ^b   Melo, Ana M P ^b,c   Saraiva, Lígia M ^b   Pereira, Manuela M ^b   Santana, Margarida ^b   Teixeira, Miguel ^b   Michel, Hartmut ^a  

^a MAX PLANCK INSTITUTE OF BIOPHYSICS   (Germany)

^b INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

^c UNIVERSIDADE LUSÓFONA DE HUMANIDADES E TECNOLOGIAS   (Portugal)

Author keywords

crystal structure; cytochrome c; multiwavelength anomalous dispersion; R. marinus

Indexed keywords

COPPER; CYTOCHROME C; ENZYME; IRON; OXIDOREDUCTASE; PROTEIN; PROTEIN SUBUNIT; RECOMBINANT PROTEIN;

ABSORPTION; ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; ATOM; BETA SHEET; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; CRYSTALLIZATION; DISPERSION; ELECTRICITY; ENZYME STRUCTURE; ESCHERICHIA COLI; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN MODIFICATION; PROTEIN STRUCTURE; RHODOTHERMUS;

ESCHERICHIA COLI; INSERTION SEQUENCES; RHODOTHERMUS MARINUS;

EID: 11844294115     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.10.069     Document Type: Article

References (39)

1. S. Ferguson-Miller, and G.T. Babcock Heme/copper terminal oxidases Chem. Rev. 96 1996 2889 2908
2. H. Michel, J. Behr, A. Harrenga, and A. Kannt Cytochrome c oxidase: structure and spectroscopy Annu. Rev. Biophys. Biomol. Struct. 27 1998 329 356
3. R.B. Gennis Coupled proton and electron transfer reactions in cytochrome oxidase Front Biosci. 9 2004 581 591
4. S. Iwata, C. Ostermeier, B. Ludwig, and H. Michel Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans Nature 376 1995 660 669
5. T. Tsukihara, H. Aoyama, E. Yamashita, T. Tomizaki, H. Yamaguchi, and K. Shinzawa-Itoh The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å Science 272 1996 1136 1144
6. J.W. Thomas, L.J. Lemieux, J.O. Alben, and R.B. Gennis Site-directed mutagenesis of highly conserved residues in helix VIII of subunit I of the cytochrome bo ubiquinol oxidase from Escherichia coli: an amphipathic transmembrane helix that may be important in conveying protons to the binuclear center Biochemistry 32 1993 11173 11180
7. J.A. Garcia-Horsman, A. Puustinen, R.B. Gennis, and M. Wikstrom Proton transfer in cytochrome bo3 ubiquinol oxidase of Escherichia coli: second-site mutations in subunit I that restore proton pumping in the mutant Asp135→Asn Biochemistry 34 1995 4428 4433
8. M.M. Pereira, M. Santana, and M. Teixeira A novel scenario for the evolution of haem-copper oxygen reductases Biochim. Biophys. Acta 1505 2001 185 208
9. M.M. Pereira, and M. Teixeira Proton pathways, ligand binding and dynamics of the catalytic site in haem-copper oxygen reductases: a comparison between the three families Biochim. Biophys. Acta 1655 2004 340 346
10. 3 terminal oxidase of the thermohalophilic bacterium Rhodothermus marinus: a HiPIP:oxygen oxidoreductase lacking the key glutamate of the D-channel Biochim. Biophys. Acta 1413 1999 1 13
11. M. Santana, M.M. Pereira, N.P. Elias, C.M. Soares, and M. Teixeira Gene cluster of Rhodothermus marinus high-potential iron-sulfur protein: oxygen oxidoreductase, a caa(3)-type oxidase belonging to the superfamily of heme-copper oxidases J. Bacteriol. 183 2001 687 699
12. M.M. Pereira, C.M. Gomes, and M. Teixeira Plasticity of proton pathways in haem-copper oxygen reductases FEBS Letters 522 2002 14 18
13. M.M. Pereira, M.L. Verkhovskaya, M. Teixeira, and M.I. Verkhovsky The caa(3) terminal oxidase of Rhodothermus marinus lacking the key glutamate of the D-channel is a proton pump Biochemistry 39 2000 6336 6340
14. M.M. Pereira, T.M. Bandeiras, A.S. Fernandes, R.S. Lemos, A.M. Melo, and M. Teixeira Respiratory chains from aerobic thermophilic prokaryotes J. Bioenerg. Biomembr. 36 2004 93 105
15. M.M. Pereira, J.N. Carita, and M. Teixeira Membrane-bound electron transfer chain of the thermohalophilic bacterium Rhodothermus marinus: a novel multihemic cytochrome bc, a new complex III Biochemistry 38 1999 1268 1275
16. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
17. R.J. Almassy, and R.E. Dickerson Pseudomonas cytochrome c551 at 2.0 Å resolution: enlargement of the cytochrome c family Proc. Natl Acad. Sci. USA 75 1978 2674 2678
18. A. Nicholls, K. Sharp, and B. Honig Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons Proteins: Struct. Funct. Genet. 11 1991 281 296
19. H.L. Axelrod, G. Feher, J.P. Allen, A.J. Chirino, M.W. Day, B.T. Hsu, and D.C. Rees Crystallization and X-ray structure determination of cytochrome c2 from Rhodobacter sphaeroides in three crystal forms Acta Crystallog. sect. D 50 1994 596 602
20. C. Frazao, C.M. Soares, M.A. Carrondo, E. Pohl, Z. Dauter, and K.S. Wilson Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin Structure 3 1995 1159 1169
21. M.E. Than, P. Hof, R. Huber, G.P. Bourenkov, H.D. Bartunik, G. Buse, and T. Soulimane T. thermophilus cytochrome-c552: a new highly thermostable cytochrome-c structure obtained by MAD phasing J. Mol. Biol. 271 1997 629 644
22. L. Holm, and C. Sander Protein structure comparison by alignment of distance matrices J. Mol. Biol. 233 1993 123 138
23. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallog. sect. A 47 1991 110 119
24. T. Schwede, J. Kopp, N. Guex, and M.C. Peitsch SWISS-MODEL: an automated protein homology-modeling server Nucl. Acids Res. 31 2003 3381 3385
25. J. Sambrook, T. Maniatis, and E.F. Fritsch Molecular Cloning. A Laboratory Manual 1982 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
26. E. Arslan, H. Schulz, R. Zufferey, P. Kunzler, and L. Thony-Meyer Overproduction of the Bradyrhizobium japonicum c-type cytochrome subunits of the cbb3 oxidase in Escherichia coli Biochem. Biophys. Res. Commun. 251 1998 744 747
27. P.M. Wood Bacterial proteins with CO-binding b- or c-type haem. Functions and absorption spectroscopy Biochim. Biophys. Acta 768 1984 293 317
28. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucl. Acids Res. 22 1994 4673 4680
29. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
30. W.A. Hendrickson Determination of macromolecular structures from anomalous diffraction of synchrotron radiation Science 254 1991 51 58
31. Collaborative Computational Project, Number 4 (1994). The CCP4 suite: programs for protein crystallography Acta Crystallog. sect. D 50 1994 760 763
32. E. De la Fortelle, and G. Bricogne Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods Methods Enzymol. 276 1997 472 494
33. G.M. Sheldrick, and T.R. Schneider SHELXL: high-resolution refinement Methods Enzymol. 277 1997 319 343
34. R.A. Laskowski, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallog. 26 1993 283 291
35. R.W. Hooft, G. Vriend, C. Sander, and E.E. Abola Errors in protein structures Nature 381 1996 272
36. P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
37. E.A. Merritt, and D.J. Bacon Raster3D: photorealistic molecular graphics Methods Enzymol. 277 1997 505 524
38. R.A. Engh, and R. Huber Accurate bond and angle parameters for X-ray protein structure refinement Acta Crystallog. sect. A A47 1991 392 400
39. R.J. Morris, A. Perrakis, and V.S. Lamzin ARP/wARP's model-building algorithms. I. The main chain Acta Crystallog. sect. D 58 2002 968 975