title: Origin, evolution and classification of type-3 copper proteins: lineage-specific gene expansions and losses across the Metazoa.
abstract: BACKGROUND
  Tyrosinases, tyrosinase-related proteins, catechol oxidases and hemocyanins comprise the type-3 copper protein family and are involved in a variety of biological processes, including pigment formation, innate immunity and oxygen transport. Although this family is present in the three domains of life, its origin and early evolution are not well understood. Previous analyses of type-3 copper proteins largely have focussed on specific animal and plant phyla.
  
  
  RESULTS
  Here, we combine genomic, phylogenetic and structural analyses to show that the original type-3 copper protein possessed a signal peptide and may have been secreted (we designate proteins of this type the α subclass). This ancestral type-3 copper protein gene underwent two duplication events, the first prior to the divergence of the unikont eukaryotic lineages and the second before the diversification of animals. The former duplication gave rise to a cytosolic form (β) and the latter to a membrane-bound form (γ). Structural comparisons reveal that the active site of α and γ forms are covered by aliphatic amino acids, and the β form has a highly conserved aromatic residue in this position. The subsequent evolution of this gene family in modern lineages of multicellular eukaryotes is typified by the loss of one or more of these three subclasses and the lineage-specific expansion of one or both of the remaining subclasses.
  
  
  CONCLUSIONS
  The diversity of type-3 copper proteins in animals and other eukaryotes is consistent with two ancient gene duplication events leading to α, β and γ subclasses, followed by the differential loss and expansion of one or more of these subclasses in specific kingdoms and phyla. This has led to many lineage-specific type-3 copper protein repertoires and in some cases the independent evolution of functionally-classified tyrosinases and hemocyanins. For example, the oxygen-carrying hemocyanins in arthropods evolved from a β-subclass tyrosinase, whilst hemocyanins in molluscs and urochordates evolved independently from an α-subclass tyrosinase. Minor conformational changes at the active site of α, β and γ forms can produce type-3 copper proteins with capacities to either carry oxygen (hemocyanins), oxidize diphenols (catechol oxidase) or o-hydroxylate monophenols (tyrosinases) and appear to underlie some functional convergences.
authors: Centre for Marine Science, School of Biological Science, The University of Queensland, Brisbane, Queensland, 4072, Australia.
authors: Felipe
authors: F
authors: Aguilera
authors: Carmel
authors: C
authors: McDougall
authors: Bernard M
authors: BM
authors: Degnan
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D004156:Catechol Oxidase / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D003300:Copper / Q000378:metabolism; D056890:Eukaryota / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D017353:Gene Deletion; D020440:Gene Duplication; D006433:Hemocyanins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D008969:Molecular Sequence Data; D014442:Monophenol Monooxygenase / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D013045:Species Specificity
chemical_list: D003300:Copper; D006433:Hemocyanins; D004156:Catechol Oxidase; D014442:Monophenol Monooxygenase
references: Mol Biol Evol. 2000 Apr;17(4):540-52
references: 10742046
references: Nat Protoc. 2009;4(3):363-71
references: 19247286
references: Science. 2011 Nov 25;334(6059):1091-7
references: 22116879
references: Nature. 2012 Oct 4;490(7418):49-54
references: 22992520
references: Protein Sci. 1999 May;8(5):978-84
references: 10338008
references: Trends Immunol. 2008 Jun;29(6):263-71
references: 18457993
references: Syst Biol. 2012 May;61(3):539-42
references: 22357727
references: Curr Biol. 2002 Aug 20;12(16):1395
references: 12194820
references: Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7774-8
references: 7644494
references: Cell Mol Life Sci. 2010 Aug;67(15):2591-603
references: 20229234
references: Nat Struct Biol. 1998 Dec;5(12):1084-90
references: 9846879
references: Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4546-51
references: 11287637
references: Pigment Cell Melanoma Res. 2009 Dec;22(6):750-60
references: 19735457
references: Syst Appl Microbiol. 2006 Jan;29(1):3-14
references: 16423650
references: Biochemistry. 2011 Jun 21;50(24):5477-86
references: 21598903
references: Trends Biochem Sci. 2000 Aug;25(8):392-7
references: 10916160
references: Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10793-7
references: 22711806
references: Pigment Cell Res. 1994 Aug;7(4):241-2
references: 7855070
references: Biol Rev Camb Philos Soc. 2011 Nov;86(4):885-99
references: 21443614
references: Nat Methods. 2011 Sep 29;8(10):785-6
references: 21959131
references: J Mol Evol. 1996 Jun;42(6):713-28
references: 8662023
references: Genome Res. 2002 Jul;12(7):1048-59
references: 12097341
references: Phytochemistry. 1997 Aug;45(7):1309-23
references: 9237394
references: Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7769-73
references: 7644493
references: Structure. 2009 May 13;17(5):749-58
references: 19446530
references: Protein Sci. 1993 Apr;2(4):597-619
references: 8518732
references: J Biol Chem. 1998 Oct 2;273(40):25889-92
references: 9748264
references: BMC Genomics. 2012 Aug 16;13:395
references: 22897796
references: Nat Rev Genet. 2008 Dec;9(12):938-50
references: 19015656
references: Proteins. 1994 Aug;19(4):302-9
references: 7984626
references: Biochim Biophys Acta. 1995 Feb 22;1247(1):1-11
references: 7873577
references: PLoS One. 2012;7(4):e35731
references: 22536431
references: J Biol Chem. 2001 May 25;276(21):17796-9
references: 11278677
references: Mol Biol Evol. 2011 Oct;28(10):2731-9
references: 21546353
references: J Agric Food Chem. 2010 Jan 27;58(2):1189-201
references: 20039636
references: J Proteome Res. 2008 Jan;7(1):209-16
references: 17988086
references: J Mol Biol. 1998 May 15;278(4):855-70
references: 9614947
references: Genomics. 1995 Sep 1;29(1):24-34
references: 8530077
references: Insect Biochem Mol Biol. 2010 Mar;40(3):166-78
references: 19932179
references: Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17002-6
references: 19805072
references: J Mol Biol. 2011 Jan 7;405(1):227-37
references: 21040728
references: Chem Rev. 1996 Nov 7;96(7):2563-2606
references: 11848837
references: Gene. 2002 Feb 20;285(1-2):59-68
references: 12039032
references: Gene. 2007 Aug 15;398(1-2):183-91
references: 17566671
references: Pigment Cell Res. 2001 Dec;14(6):428-36
references: 11775054
references: Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10545-8
references: 12149441
references: J Exp Biol. 1998 Apr;201(Pt 8):1085-98
references: 9510522
references: Bioinformatics. 2011 Apr 15;27(8):1164-5
references: 21335321
references: Adv Protein Chem. 1995;47:1-81
references: 8561049
references: Curr Biol. 2011 Nov 8;21(21):R877-83
references: 22075424
references: Mol Biol Evol. 2009 Aug;26(8):1851-64
references: 19414522
references: Comp Biochem Physiol B Biochem Mol Biol. 2007 Feb;146(2):207-14
references: 17150393
references: Bioinformatics. 2001 Sep;17(9):847-8
references: 11590104
references: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references: 9254694
references: Mol Biol Evol. 2007 Sep;24(9):1934-43
references: 17569752
references: J Biol Chem. 2001 May 11;276(19):15563-6
references: 11279230
references: Bioinformatics. 2010 Dec 1;26(23):2983-5
references: 20937596
references: J Exp Biol. 2000 Jun;203(Pt 12):1777-82
references: 10821735
references: Comp Biochem Physiol B Biochem Mol Biol. 2008 Mar;149(3):439-46
references: 18162195
references: J Biol Chem. 2006 Mar 31;281(13):8981-90
references: 16436386
references: J Comp Physiol B. 2002 Feb;172(2):95-107
references: 11916114
references: Biochem Biophys Res Commun. 2006 Apr 7;342(2):632-9
references: 16488396
references: Nucleic Acids Res. 2005 Jan 20;33(2):511-8
references: 15661851
references: Syst Biol. 2010 May;59(3):307-21
references: 20525638
references: Pigment Cell Res. 1994 Dec;7(6):388-93
references: 7761346
references: J Biol Chem. 1994 May 27;269(21):14939-45
references: 8195126