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. 2009 Aug 11;284(43):29757–29772. doi: 10.1074/jbc.M109.038513

FIGURE 1.

FIGURE 1.

Protein organization and GAF domain amino acid sequence alignment of representative Cycs. A, domain architectures of representative Cycs as compared with the Cph Syn-Cph1 and the PAS-less Phy SyB-Cph1. EBD, ethylene-binding; HAMP, histidine kinase/adenyl cyclase/methyl-binding protein/phosphatase; MA, methyl-accepting; TM, predicted transmembrane. The motifs containing the cysteine(s) that bind(s) the bilin and the histidine in the HK domain that participates in phosphotransfer are indicated. B, alignment of the GAF domain from representative Cycs (brackets) with members of the BphP (Dr-BphP), Cph (Syn-Cph1), PAS-less Phy (SyB-Cph1), and plant Phy (At-PhyA) clades. The predicted α-helical and β strand secondary structures based on the Dr-BphP and SyB-Cph1 three-dimensional structures (5, 8) are shown above the alignment. The bracket locates the conserved knot lasso loop present in canonical Phys. The dashed line locates the Cyc-specific motif bearing the second bilin attachment site. The two cysteines (Cys-494 and Cys-522) that bind the bilin are indicated by the closed arrowheads. Other key residues, some of which impact the spectral properties of Te-PixJ, are indicated by the open arrowheads. The amino acid numbering refers to the Te-PixJ sequence. Sequences in the alignment include: Te-PixJ from T. elongatus BP-1 (Tll0569), Syn-PixJ(TaxD1) from Synechocystis sp. PCC6803 (Sll0041), ZP_01728273 from Cyanothece sp. CCY0110, AM1_0048 from A. marina (MBIC11017), Glr3432 from G. violaceus PCC7421, Syn-Etr1 from Synechocystis sp. PCC6803 (Slr1212), Te-CikA from T. elongatus BP-1 (Tll0899), Syn-CikA from S. elongatus (slr1969), Ana-CikA from A. variabilis ATCC 29413 (Ava_1168), An(Nos)-PixJ from Anabena (Nostoc) sp. PCC7120 (All1069), RcaE from F. diplosiphon (AAB08575), SyB-Cph1 from Synechococcus sp. JA-2-3B′a(2-13) (CYB_2465), Dr-BphP from D. radiodurans R1 (DR0050), Syn-Cph1 from Synechocystis sp. PCC6803 (Slr0473), and At-PhyA from A. thaliana Columbia-0 ecotype (At1g09570). The accession numbers or locus tags are in parentheses.