Characterization of a prokaryotic haemerythrin from the methanotrophic bacterium Methylococcus capsulatus (Bath)

FEBS Journal

Volumn 272, Issue 10, 2005, Pages 2428-2440

  Karlsen, Odd A ^a   Ramsevik, Linda ^a   Bruseth, Live J ^a   Larsen, Øivind ^a   Brenner, Annette ^a   Berven, Frode S ^a   Jensen, Harald B ^a   Lillehaug, Johan R ^a  

^a UNIVERSITY OF BERGEN   (Norway)

Author keywords

Copper regulated; Methanotroph; Methylococcus capsulatus; Prokaryotic haemerythrin; Two dimensional gel electrophoresis

Indexed keywords

ASPARTIC ACID; BACTERIAL PROTEIN; CARBOXYLIC ACID DERIVATIVE; GLUTAMIC ACID; HEMERYTHRIN; HISTIDINE; HYBRID PROTEIN; IRON; ISOLEUCINE; LEUCINE; METHANE; OXYGEN; PHENYLALANINE; RECOMBINANT PROTEIN; TRYPTOPHAN;

ARTICLE; BACTERIAL GROWTH; BACTERIUM CULTURE; BIOMASS; ESCHERICHIA COLI; GENE EXPRESSION; GENETIC CONSERVATION; HYDROPHOBICITY; INVERTEBRATE; MARINE ENVIRONMENT; METHANOTROPHIC BACTERIUM; METHYLOCOCCUS CAPSULATUS; MICROBIAL BIOMASS; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FOLDING; SEQUENCE HOMOLOGY; ULTRAVIOLET SPECTROPHOTOMETRY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; CLONING, MOLECULAR; HEMERYTHRIN; METALS; METHYLOCOCCUS CAPSULATUS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT FUSION PROTEINS; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; INVERTEBRATA; METHYLOCOCCUS CAPSULATUS; PROKARYOTA;

EID: 18944380045     PISSN: 1742464X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2005.04663.x     Document Type: Article

References (50)

1. Stenkamp RE (1994) Dioxygen and Hemerythrin. Chem Rev 94, 715-726.
2. 2 carriers in blood and tissues. In Advances in Comparative and Environmental Physiology (Mangum CP, ed), pp. 151-171. Springer Verlag, Heidelberg.
3. Xiong J, Kurtz DM Jr, Ai J & Sanders-Loehr J (2000) A hemerythrin-like domain in a bacterial chemotaxis protein. Biochemistry 39, 5117-5125.
4. Kao WC, Chen YR, Yi EC, Lee H, Tian Q, Wu KM, Tsai SF, Yu SS, Chen YJ, Aebersold R & Chan SI (2004) Quantitative proteomic analysis of metabolic regulation by copper ions in methylococcus capsulatus (Bath). J Biol Chem 279, 51554-51560.
5. Ward N, Larsen E, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH et al. (2004) Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath). Plos Biol 2, E303.
6. Gattiker A, Gasteiger E & Bairoch A (2002) ScanProsite: a reference implementation of a PROSITE scanning tool. Appl Bioinformatics 1, 107-108.
7. Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ et al. (2003) CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res 31, 383-387.
8. Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY & Bryant SH (2002) CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 30, 281-283.
9. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F & Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
10. Schwede T, Kopp J, Guex N & Peitsch MC (2003) SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res 31, 3381-3385.
11. Martins LJ, Hill CP & Ellis WR Jr (1997) Structures of wild-type chloromet and L103N hydroxomet Themiste zostericola myohemerythrins at 1.8 Å resolution. Biochemistry 36, 7044-7049.
12. Zhang JH, Kurtz DM Jr, Xia YM & Debrunner PG (1991) Reconstitution of the diiron sites in hemerythrin and myohemerythrin. Biochemistry 30, 583-589.
13. Gupta N, Bonomi F, Kurtz DM Jr, Ravi N, Wang DL & Huynh BH (1995) Recombinant Desulfovibrio vulgaris rubrerythrin. Isolation and characterization of the diiron domain. Biochemistry 34, 3310-3318.
14. Nielsen AK, Gerdes K & Murrell JC (1997) Copper-dependent reciprocal transcriptional regulation of methane mono-oxygenase genes in Methylococcus capsulatus and Methylosinus trichosporium. Mol Microbiol 25, 399-409.
15. Nielsen AK, Gerdes K, Degn H & Murrell JC (1996) Regulation of bacterial methane oxidation: transcription of the soluble methane mono-oxygenase operon of Methylococcus capsulatus (Bath) is repressed by copper ions. Microbiology 142, 1289-1296.
16. Stanley SH, Prior SD, Leak DJ & Dalton H (1983) Copper stress underlies the fundamental change in intracellular location of the methane mono-oxygenase in methane-oxidizing organisms: studies in batch and continuous cultures. Biotechnol Lett 5, 487-492.
17. Prior SD & Dalton H (1985) The effect of copper ions on the membrane content and methane mono-oxygenase activity in methanol-grown Methylococcus capsulatus. Journal Gen Microbiol 131, 155-163.
18. Murrell JC, McDonald IR & Gilbert B (2000) Regulation of expression of methane mono-oxygenases by copper ions. Trends Microbiol 8, 221-225.
19. Sheriff S, Hendrickson WA & Smith JL (1987) Structure of myohemerythrin in the azidomet state at 1.7/1.3 Å resolution. J Mol Biol 197, 273-296.
20. 2 binding pocket. J Biol Inorg Chem 6, 418-429.
21. Zhang JH & Kurtz DM Jr (1992) Metal substitutions at the diiron sites of hemerythrin and myohemerythrin: contributions of divalent metals to stability of a four-helix bundle protein. Proc Natl Acad Sci USA 89, 7065-7069.
22. Terwilliger NB (1998) Functional adaptations of oxygen-transport proteins. J Exp Biol 201, 1085-1098.
23. Chan SI, Chen KH, Yu SS, Chen CL & Kuo SS (2004) Toward delineating the structure and function of the particulate methane monooxygenase from methanotrophic bacteria. Biochemistry 43, 4421-4430.
24. Whittenbury R, Phillips KC & Wilkinson JF (1970) Enrichment, isolation and some properties of methane-utilizing bacteria. J General Microbiol 61, 205-218.
25. Brusseau GA, Tsien HC, Hanson RS & Wackett LP (1990) Optimization of trichloroethylene oxidation by methanotrophs and the use of a colorimetric assay to detect soluble methane mono-oxygenase activity. Biodegradation 1, 19-29.
26. Fjellbirkeland A, Kleivdal H, Joergensen C, Thestrup H & Jensen HB (1997) Outer membrane proteins of Methylococcus capsulatus (Bath). Arch Microbiol 168, 128-135.
27. Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685.
28. Rabilloud T, Adessi C, Giraudel A & Lunardi J (1997) Improvement of the solubilization of proteins in two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 18, 307-316.
29. De Marco V, Stier G, Blandin S & de Marco A (2004) The solubility and stability of recombinant proteins are increased by their fusion to NusA. Biochem Biophys Res Commun 322, 766-771.
30. Bohm G, Muhr R & Jaenicke R (1992) Quantitative analysis of protein far UV circular dichroism spectra by neural networks. Protein Eng 5, 191-195.
31. Sambrook J, Fritsch EF & Maniatis T (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
32. Morris AL, MacArthur MW, Hutchinson EG & Thornton JM (1992) Stereochemical quality of protein structure coordinates. Proteins 12, 345-364.
33. Laskowski R, MacArthur M, Moss D & Thornton J (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26, 283-291.
34. Luthy R, Bowie JU & Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356, 83-85.
35. Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17, 355-362.
36. Pollastri G, Przybylski D, Rost B & Baldi P (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47, 228-235.
37. Rost B & Sander C (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19, 55-72.
38. McGuffin LJ, Bryson K & Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16, 404-405.
39. Klippenstein GL, Holleman JW & Klotz IM (1968) The primary structure of Golfingia gouldii hemerythrin. Oder of peptides in fragments produced by tryptic digestion of succinylated hemerythrin. Complete amino acid sequence. Biochemistry 7, 3868-3878.
40. Ferrell RE & Kitto GB (1971) Structural studies on Dendrostomum pyroides hemerythrin. Biochemistry 10, 2923-2929.
41. Loehr JS, Lammers PJ, Brimhall B & Hermodson MA (1978) Amino acid sequence of hemerythrin from Themiste dyscritum. J Biol Chem 253, 5726-5731.
42. Uchida T, Yano H, Satake K, Kubota I & Tsugita A (1990) The amino acid sequence of hemerythrin from Siphonosoma cumanense. Protein Seq Data Anal 3, 141-147.
43. Yano H, Satake K, Ueno Y & Tsugita A (1991) The amino acid sequence of the beta chain of hemerythrin from Lingula unguis. Protein Seq Data Anal 4, 87-91.
44. Yano H, Satake K, Ueno Y, Kondo K & Tsugita A (1991) Amino acid sequence of the hemerythrin alpha subunit from Lingula unguis. J Biochem (Tokyo) 110, 376-380.
45. Negri A, Tedeschi G, Bonomi F, Zhang JH & Kurtz DM Jr (1994) Amino-acid sequences of the alpha- and beta-subunits of hemerythrin from Lingula reevii. Biochim Biophys Acta 1208, 277-285.
46. Long RC, Zhang JH, Kurtz DM Jr, Negri A, Tedeschi G & Bonomi F (1992) Myohemerythrin from the sipunculid, Phascolopsis gouldii: purification, properties and amino acid sequence. Biochim Biophys Acta 1122, 136-142.
47. Klippenstein GL, Cote JL & Ludlam SE (1976) The primary structure of myohemerythrin. Biochemistry 15, 1128-1136.
48. Goutte L, Slomianny MC, Malecha J & Baert JL (2001) Cloning and expression analysis of a cDNA that encodes a leech hemerythrin. Biochim Biophys Acta 1518, 282-286.
49. Demuynck S, Li KW, Van der Schors R & Dhainaut-Courtois N (1993) Amino acid sequence of the small cadmium-binding protein (MP II) from Nereis diversicolor (annelida, polychaeta). Evidence for a myohemerythrin structure. Eur J Biochem 217, 151-156.
50. Takagi T & Cox JA (1991) Primary structure of myohemerythrin from the annelid Nereis diversicolor. FEBS Lett 285, 25-27.