TABLE 2.
Protein | Loop I | Loop II | Loop III | Loop IV |
---|---|---|---|---|
Laccases | ||||
Phanerocaete chrysosporium MCO1 | LNAQYLSPSGPIGGSA | TLQQTDMFTYKLPGQNPD-N | FDNLPSGASRAYM | VLDLVLENNDNGD |
Cryptococcus neoformans Lac | IIAALATPEGYKGNIA | T--SVA-LSCMFGAVSQE-G | -NVLGNTFQGYGF | ---T-VI---D-- |
Cucumis cinereus Lac | -IPA---P-SIQG--A | AQPNKG-RNGLAGTFANGVN | --QLGFSGGRFTI | ---AGVL---GGP |
Trametes villosa Lcc3 | -TPA------PL---- | ANPNRANTTGFANGI----N | ----TFNGSEFFI | ---GGVT---GGP |
Ceriporiopsis subvermispora Lcs-1 | -AAA-----STLT--F | ANPNNG-NMGFANGI----N | ----TFNGTNLFI | ---GNII---AGP |
Agaricus bisporus Lcc-1 | -ILAPDATNEFFSSGI | A-PMTGGNPDRNPNLNISLT | ---AQPNAPFFDI | ---G------EGA |
Thanatephorus cucumeris Lac4 | -VLEKQMFSTNNTALL | A-PMTVAGAGTNANLDPTNV | -RSTVDGILRFTF | ---HHR----GAD |
Cryptococcus parasiticus Lac | -TAD--ELVVYTQSNA | VTFGGGGFCGKSNNPY---P | ----STTTRKWTI | ---ATGN---ALP |
Pleurotus ostreatus Pox1 | -VVA-------PQNAV | ADPNLG-STGFDGGI----N | --AFDVTNFELTI | ---ALAV---GGP |
Trametes versicolor Lac3 | -VAA------NVGPAF | ANPNFG-NVGFTGGI----N | ----NFNGTNFFI | ---ATAA-APGAP |
Trametes versicolor Lcc2 | -TAA------RLGPRF | ANPNFG-TVGFAGGI----N | ----NFNGTNFFI | ---ATAL-APGAP |
Nicotiana tabacum Lac | -TEAVINEAIKSGLA- | ASPFMDAPIAVDNVT----A | MPTVALLQAHFFG | ---DTGIIAPEN- |
Melanocarpus albomyces Lac | -RAA-DDLVHFTQNNA | VTFGGQAACGGSLNPH---P | -DLTGTPLFVWKV | ---EGPF---SLP |
Class | ---------------- | -------------------- | ------------- | --------XX--- |
All | ---------------- | -------------------- | ------------- | ------------- |
Ascorbate oxidases | ||||
Phanerochaete chrysosporium MCO1 | LNAQYL-S-PSGPIGGSAG | TLQQTDMFTYKLPGQNPDN | FDNLPSGASRAY | VLDLVLENNDNGD |
Cucurbita pepo LaoZ | QEVG-LSSKPIRWIGEPQ- | TRARHPNTPPGLTLLNYLP | LPPTPYLGAMKY | QNANMMKENLSET |
Arabidopsis thaliana AOZ | QELA-LSSRPMRWIGEPQ- | VRGREPKTPQALTVINYVD | VPVTPYLGSIRY | QNANVLKGVISEI |
Cucurbita melo AOZ | QEVG-LKSNPMRWIGELQ- | VRGRKPKTSPALLLFNYLP | LPSTPYLGAIKF | QNANALTNNTSEI |
Medicago truncatula AOZ | QEVG-LSSAPMRWIGEPQ- | VRGRKPSTPQALTILNYKP | LPTTPYLGSIKF | QNANQLNGNGSEI |
Nicotiana tabacum AOZ | QEVD-LSSNPLRWIGEPQ- | VRGREPKTPQGLTLLNYLP | LPTQLYLGSIRY | QNANALAKDVSEI |
Class | XX---X-X-X-XXXXX-X- | -X-X-X-X---X---XX-- | -X---XXX---- | XXXX------XX- |
All | -----O-O-O---OO---- | -----------O---O--- | ------------ | ------------- |
Ferroxidases | ||||
Phanerochaete chrysosporium MCO1 | L-NAQYLSPSGPIGGSA | TLQQTDMFTYKLPGQNPDN | FDNLPSGASRAY | VLDLVLENNDNGD |
Neurospora crassa Fet3 | L-QPRFMSKYNP----T | ASMDTTLFDT-IPPGLNTN | MNNLASGANYAF | IVQIVLNNLDSGR |
Arrula adeninivorans Fet3 | LNKEEFLTLYNP----T | SIFDENLFDV-IPSDLGMN | MTNLDNGVNYAF | VVEIVVNNNDAGF |
Saccharomyces cerevisiae Fet3 | L-IPNFMSRFNP----T | QRVDDTMLDV-IPKDLELN | MDNLDDGVNYAF | VIEIVLNNLDTGK |
Schizocaccharomyces pombe Fet3 | LVPDEFKTWKNP----T | AYMDESLFDT-IPDNYNPN | FFTLGDGANYAE | VVDVIIDNHDTGK |
Candida albicans Fet3 | I-GPAFLTRFNP----T | NGVDTTMLDS-VPADLQVN | MNVLNDGINYAF | IVDIVLNNFDTGK |
Saccharomyces cerevisiae Fet3 | L-TKSFMSVYNP----T | QKFDDTMLDV-IPSDLQLN | MDNLKNGVNYAF | IVEIVLNNQDTGT |
Class | -----X----XX----X | ---X----X---X-----X | ---X---X-XXX- | -------X-X-X- |
All | -----------O----- | ------------O-----O | ---O--O---O- | -------O-O-O- |
Within each class of MCOs (laccases, ascorbate oxidases, and ferroxidases), a subset of sequences, excluding close protein homologues, was selected and aligned. Multiple alignments containing the selected sequences for each class were independently realigned with the MCO1 sequence. The MCO1 regions predicted to be in contact with the substrate ligand (Table 1) were mapped in these multiple alignments, which allowed identification of the corresponding regions in laccases, ascorbate oxidases, and ferroxidases. For each protein class, conserved identical residues within the group of selected sequences are indicated by X. Residues conserved in each group and in the MCO1 sequence are indicated by boldface type and by O in the alignment.