Phycobilin:cystein-84 biliprotein lyase, a near-universal lyase for cysteine-84 binding sites in cyanobacterial biliproteins

College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 10/2007; 104(36):14300-5. DOI: 10.1073/pnas.0706209104
Source: PubMed


Phycobilisomes, the light-harvesting complexes of cyanobacteria and red algae, contain two to four types of chromophores that are attached covalently to seven or more members of a family of homologous proteins, each carrying one to four binding sites. Chromophore binding to apoproteins is catalyzed by lyases, of which only few have been characterized in detail. The situation is complicated by nonenzymatic background binding to some apoproteins. Using a modular multiplasmidic expression-reconstitution assay in Escherichia coli with low background binding, phycobilin:cystein-84 biliprotein lyase (CpeS1) from Anabaena PCC7120, has been characterized as a nearly universal lyase for the cysteine-84-binding site that is conserved in all biliproteins. It catalyzes covalent attachment of phycocyanobilin to all allophycocyanin subunits and to cysteine-84 in the beta-subunits of C-phycocyanin and phycoerythrocyanin. Together with the known lyases, it can thereby account for chromophore binding to all binding sites of the phycobiliproteins of Anabaena PCC7120. Moreover, it catalyzes the attachment of phycoerythrobilin to cysteine-84 of both subunits of C-phycoerythrin. The only exceptions not served by CpeS1 among the cysteine-84 sites are the alpha-subunits from phycocyanin and phycoerythrocyanin, which, by sequence analyses, have been defined as members of a subclass that is served by the more specialized E/F type lyases.

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    • "Among those which have been biochemically characterized, most are highly specific in vivo as they can ligate only one phycobilin type at one particular PBP binding site. However, CpcS (a member of the S/U clan) can bind either PCB or PEB to one specific site, Cys-82 (consensus numbering), of a variety of PBPs (α- and β-APC and PE, β-PC and PEC) and is therefore more universal (8). Furthermore, some enzymes of the E/F clan are bifunctional, because they can both bind a chromophore (either PCB for PecE/F or PEB for RpcG) to α-PC and change its chemical configuration into another isomer [i.e. "
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    ABSTRACT: CyanoLyase ( is a manually curated sequence and motif database of phycobilin lyases and related proteins. These enzymes catalyze the covalent ligation of chromophores (phycobilins) to specific binding sites of phycobiliproteins (PBPs). The latter constitute the building bricks of phycobilisomes, the major light-harvesting systems of cyanobacteria and red algae. Phycobilin lyases sequences are poorly annotated in public databases. Sequences included in CyanoLyase were retrieved from all available genomes of these organisms and a few others by similarity searches using biochemically characterized enzyme sequences and then classified into 3 clans and 32 families. Amino acid motifs were computed for each family using Protomata learner. CyanoLyase also includes BLAST and a novel pattern matching tool (Protomatch) that allow users to rapidly retrieve and annotate lyases from any new genome. In addition, it provides phylogenetic analyses of all phycobilin lyases families, describes their function, their presence/absence in all genomes of the database (phyletic profiles) and predicts the chromophorylation of PBPs in each strain. The site also includes a thorough bibliography about phycobilin lyases and genomes included in the database. This resource should be useful to scientists and companies interested in natural or artificial PBPs, which have a number of biotechnological applications, notably as fluorescent markers.
    Full-text · Article · Jan 2013 · Nucleic Acids Research
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    • "Fig 1: Structures of free (Left) and bound (Right) PCB and PEB. (Complied by Zhao et al., 2007 [23] "

    Full-text · Article · Apr 2012
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    • "), it was soluble and, moreover, allowed for subsequent chromophorylation in vitro at the ApcE site. The singly chromophorylated ApcE(1–240/Δ87– 130)::PCB-RpcA(35–162) was purified by Ni 2+ affinity chromatography , and then treated with fresh PCB derived from the supernatant of broken cells of E. coli that produced PCB in the presence of pACYC- ho1-pcyA [22] [32]. The absorption spectrum of the resulting product had the two bands at 660 and 612 nm expected for the doubly chromophorylated PCB-ApcE(1–240/Δ87–130)::PCB-RpcA(35–162) (Fig. 2C). "
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    ABSTRACT: Phycobilisomes, the light-harvesting antennas in cyanobacteria and red algae, consist of an allophycocyanin core that is attached to the membrane via a core-membrane linker, and rods comprised of phycocyanin and often also phycoerythrin or phycoerythrocyanin. Phycobiliproteins show excellent energy transfer among the chromophores that renders them biomarkers with large Stokes-shifts absorbing over most of the visible spectrum and into the near infrared. Their application is limited, however, due to covalent binding of the chromophores and by solubility problems. We report construction of a water-soluble minimal chromophore-binding unit of the red-absorbing and fluorescing core-membrane linker. This was fused to minimal chromophore-binding units of phycocyanin. After double chromophorylation with phycocyanobilin, in E. coli, the fused phycobiliproteins absorbed light in the range of 610-660nm, and fluoresced at ~670nm, similar to phycobilisomes devoid of phycoerythr(ocyan)in. The fused phycobiliprotein could also be doubly chromophorylated with phycoerythrobilin, resulting in a chromoprotein absorbing around 540-575nm, and fluorescing at ~585nm. The broad absorptions and the large Stokes shifts render these chromoproteins candidates for imaging; they may also be helpful in studying phycobilisome assembly.
    Full-text · Article · Mar 2012 · Biochimica et Biophysica Acta
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