Phylogenetic Analysis of Six-Domain Multi-Copper Blue Proteins

PLoS Currents

Volumn , Issue MARCH 2013, 2013, Pages

  Vasin, Andrey ^a   Klotchenko, Sergey ^a   Puchkova, Ludmila ^b  

^a Reseach Institute of Influenza   (Russian Federation)

^b PETER THE GREAT ST PETERSBURG POLYTECHNIC UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BLOOD CLOTTING FACTOR 5; BLOOD CLOTTING FACTOR 8; CERULOPLASMIN; COPPER PROTEIN; HEPHAESTIN;

ALGA; AMINO ACID SUBSTITUTION; ARTICLE; BINDING SITE; CHLAMYDOMONAS REINHARDTII; DUNALIELLA SALINA; GENETIC VARIABILITY; HALORUBRUM LACUSPROFUNDI; INVERTEBRATE; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PROTEIN DOMAIN; PROTEIN LOCALIZATION; SEQUENCE ALIGNMENT;

EID: 84875462137     PISSN: None     EISSN: 21573999     Source Type: Journal    
DOI: 10.1371/currents.tol.574bcb0f133fe52835911abc4e296141     Document Type: Article

References (32)

1. Messerschmidt A, Huber R. The blue oxidases, ascorbate oxidase, laccase and ceruloplasmin. Modelling and structural relationships. Eur J Biochem. 1990 Jan 26;187(2):341-52. PubMed PMID:2404764. 2404764.
2. Adman ET, Murphy MEP. Copper nitrite reductase, in: Messerschmidt, A., Huber M., Poulos, T., Wieghardt, K. (Eds.) Handbook on Metalloproteins. 2001; Chichester [etc.]: John Wiley & Sons, pp. 1381-1390.
3. Solomon EI, Sundaram UM, Machonkin TE. Multicopper Oxidases and Oxygenases. Chem Rev. 1996 Nov 7;96(7):2563-2606. PubMed PMID:11848837. 11848837.
4. Nakamura K, Go N. Function and molecular evolution of multicopper blue proteins. Cell Mol Life Sci. 2005 Sep;62(18):2050-66. PubMed PMID:16091847. 16091847.
5. Murphy ME, Lindley PF, Adman ET. Structural comparison of cupredoxin domains: domain recycling to construct proteins with novel functions. Protein Sci. 1997 Apr;6(4):761-70. PubMed PMID:9098885. 9098885.
6. Zaitseva I, Zaitsev V, Card G, Moshkov K, Bax B, Ralph A, Lindley P. The nature of the copper centers in human ceruloplasmin. J Biol Inorg Chem. 1996; 1:15-22.
7. Nersissian AM, Shipp EL. Blue copper-binding domains. Adv Protein Chem. 2002;60:271-340. PubMed PMID:12418180. 12418180.
8. Zaitsev VN, Zaitseva I, Papiz M, Lindley PF. An X-ray crystallographic study of the binding sites of the azide inhibitor and organic substrates to ceruloplasmin, a multi-copper oxidase in the plasma. J Biol Inorg Chem. 1999 Oct;4(5):579-87. PubMed PMID:10550686. 10550686.
9. Askwith C, Eide D, Van Ho A, Bernard PS, Li L, Davis-Kaplan S, Sipe DM, Kaplan J. The FET3 gene of S. cerevisiae encodes a multicopper oxidase required for ferrous iron uptake. Cell. 1994 Jan 28;76(2):403-10. PubMed PMID:8293473. 8293473.
10. Alexandre G, Zhulin IB. Laccases are widespread in bacteria. Trends Biotechnol. 2000 Feb;18(2):41-2. PubMed PMID:10652504. 10652504.
11. Dittmer NT, Suderman RJ, Jiang H, Zhu YC, Gorman MJ, Kramer KJ, Kanost MR. Characterization of cDNAs encoding putative laccase-like multicopper oxidases and developmental expression in the tobacco hornworm, Manduca sexta, and the malaria mosquito, Anopheles gambiae. Insect Biochem Mol Biol. 2004 Jan;34(1):29-41. PubMed PMID:14723895. 14723895.
12. Bielli P, Calabrese L. Structure to function relationships in ceruloplasmin: a 9moonlighting9 protein. Cell Mol Life Sci. 2002 Sep;59(9):1413-27. PubMed PMID:12440766. 12440766.
13. Vasin AV, Platonova NA, Povalikhin RG, Klotchenko SA, Samsonov SA, Tsymbalenko NV, Puchkova LV. [Mitochondrial ceruloplasmin of mammals]. Mol Biol (Mosk). 2005 Jan-Feb;39(1):48-60. PubMed PMID:15773547. 15773547.
14. Stoj C, Kosman DJ. Cuprous oxidase activity of yeast Fet3p and human ceruloplasmin: implication for function. FEBS Lett. 2003 Nov 20;554(3):422-6. PubMed PMID:14623105. 14623105.
15. Rydén L. Single-chain structure of human ceruloplasmin. Eur J Biochem. 1972 Apr 11;26(3):380-6. PubMed PMID:5036973. 5036973.
16. Vasiliev VB, Shavlovsky MM, Neifakh SA, Prozorovsky VN, Rashkovetsky LG. Intramolecular homology in human ceruloplasmin. Russ Jour Bioorg Chem 1979;5:1045-52.
17. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10. PubMed PMID:2231712. 2231712.
18. Galtier N, Gouy M, Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci. 1996 Dec;12(6):543-8. PubMed PMID:9021275. 9021275.
19. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792-7. PubMed PMID:15034147. 15034147.
20. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999; 41:95-98.
21. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007 Aug;24(8):1596-9. PubMed PMID:17488738. 17488738.
22. Nei M, Kumar S. Molecular evolution and phylogenetics. Oxford University Press 2000.
23. Gaǐtskhoki VS, Voronina OV, Denezhkina VV, Pliss MG, Puchkova LV, Shvartsman AL, Neǐfakh SA. [Expression of ceruloplasmin gene in various organs of the rat]. Biokhimiia. 1990 May;55(5):927-37. PubMed PMID:2393680. 2393680.
24. Schwartzman AL, Gaitskhoki VS, L'vov VM, Nosikov VV, Braga EM, Frolova LYu, Skobeleva NA, Kisselev LL, Neifakh SA. Complex molecular structure of the gene coding for rat ceruloplasmin. Gene. 1980 Oct;11(1-2):1-10. PubMed PMID:6254847. 6254847.
25. Takahashi N, Ortel TL, Putnam FW. Single-chain structure of human ceruloplasmin: the complete amino acid sequence of the whole molecule. Proc Natl Acad Sci U S A. 1984 Jan;81(2):390-4. PubMed PMID:6582496. 6582496.
26. Rao VS, Kini RM. Pseutarin C, a prothrombin activator from Pseudonaja textilis venom: its structural and functional similarity to mammalian coagulation factor Xa-Va complex. Thromb Haemost. 2002 Oct;88(4):611-9. PubMed PMID:12362232. 12362232.
27. Welton RE, Burnell JN. Full length nucleotide sequence of a factor V-like subunit of oscutarin from Oxyuranus scutellatus scutellatus (coastal Taipan). Toxicon. 2005 Sep 1;46(3):328-36. PubMed PMID:15993914. 15993914.
28. La Fontaine S, Quinn JM, Nakamoto SS, Page MD, Göhre V, Moseley JL, Kropat J, Merchant S. Copper-dependent iron assimilation pathway in the model photosynthetic eukaryote Chlamydomonas reinhardtii. Eukaryot Cell. 2002 Oct;1(5):736-57. PubMed PMID:12455693. 12455693.
29. van Waasbergen LG, Hildebrand M, Tebo BM. Identification and characterization of a gene cluster involved in manganese oxidation by spores of the marine Bacillus sp. strain SG-1. J Bacteriol. 1996 Jun;178(12):3517-30. PubMed PMID:8655549. 8655549.
30. Nakamura K, Kawabata T, Yura K, Go N. Novel types of two-domain multi-copper oxidases: possible missing links in the evolution. FEBS Lett. 2003 Oct 23;553(3):239-44. PubMed PMID:14572631. 14572631.
31. Rydén LG, Hunt LT. Evolution of protein complexity: the blue copper-containing oxidases and related proteins. J Mol Evol. 1993 Jan;36(1):41-66. PubMed PMID:8433378. 8433378.
32. Francis CA, Tebo BM. Enzymatic manganese(II) oxidation by metabolically dormant spores of diverse Bacillus species. Appl Environ Microbiol. 2002 Feb;68(2):874-80. PubMed PMID:11823231. 11823231.