CyanoLyase: A database of phycobilin lyase sequences, motifs and functions

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Bretaudeau, Anthony ^a   Coste, François ^a   Humily, Florian ^b,c   Garczarek, Laurence ^b,c   Le Corguillé, Gildas ^b,d   Six, Christophe ^b,c   Ratin, Morgane ^b,c   Collin, Olivier ^a   Schluchter, Wendy M ^e   Partensky, Frédéric ^b,c  

^a CAMPUS DE BEAULIEU   (France)

^b SORBONNE UNIVERSITÉ   (France)

^c STATION BIOLOGIQUE DE ROSCOFF   (France)

^d STATION BIOLOGIQUE   (France)

^e University of New Orleans   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LYASE; PHYCOBILIN LYASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CYANOBACTERIUM; DATA ANALYSIS; ENZYME ACTIVITY; GENETIC DATABASE; GENOME ANALYSIS; INFORMATION RETRIEVAL; PHYLOGENY; PRIORITY JOURNAL; PROTEIN MOTIF; RED ALGA; SEQUENCE DATABASE; SEQUENCE HOMOLOGY;

AMINO ACID MOTIFS; CYANOBACTERIA; DATABASES, PROTEIN; INTERNET; LYASES; MOLECULAR SEQUENCE ANNOTATION; PHYCOBILINS; PHYCOBILIPROTEINS; RHODOPHYTA; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

CYANOBACTERIA; RHODOPHYTA;

EID: 84876569399     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1091     Document Type: Article

References (27)

1. Apt, K.E., Collier, J.L. and Grossman, A.R. (1995) Evolution of the phycobiliproteins. J. Mol. Biol., 248, 79-96.
2. Glazer, A.N. (1982) Phycobilisomes: structure and dynamics. Annu. Rev. Microbiol., 36, 173-198.
3. Sidler, W.A. (1994) Phycobilisome and phycobiliprotein structure. In: Bryant, D.A. (ed.), The Molecular Biology of Cyanobacteria. Kluwer Academic Publishers, The Netherlands, pp. 139-216.
4. Glazer, A.N. and Wedemayer, G.J. (1995) Cryptomonad biliproteins - an evolutionary perspective. Photosynth. Res., 46, 93-105.
5. Six, C., Thomas, J.C., Garczarek, L., Ostrowski, M., Dufresne, A., Blot, N., Scanlan, D.J. and Partensky, F. (2007) Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study. Genome Biol., 8, R259.
6. Scheer, H. and Zhao, K.H. (2008) Biliprotein maturation: the chromophore attachment. Mol. Microbiol., 68, 263-276.
7. Schluchter, W.M., Shen, G., Alvey, R.M., Biswas, A., Saunee, N.A., Williams, S.R., Miller, C.A. and Bryant, D.A. (2010) Phycobiliprotein biosynthesis in cyanobacteria: structure and function of enzymes involved in post-translational modification. Adv. Exp. Med. Biol., 675, 211-228.
8. Zhao, K., Su, P., Tu, J., Wang, X., Liu, H., Ploscher, M., Eichacker, L., Yang, B., Zhou, M. and Scheer, H. (2007) Phycobilin: cystein-84 biliprotein lyase, a near-universal lyase for cysteine-84-binding sites in cyanobacterial phycobiliproteins. Proc. Natl Acad. Sci. USA, 104, 14300-14305.
9. Blot, N., Wu, X.-J., Thomas, J.-C., Zhang, J., Garczarek, L., Bohm, S., Tu, J.M., Zhou, M., Plöscher, M., Eichacker, L. et al. (2009) Phycourobilin in a unique trichromatic phycobiliprotein is formed post-translationally by a novel phycoerythrobilin lyase-isomerase. J. Biol. Chem., 284, 9290-9298.
10. Jung, L.J., Chan, C.F. and Glazer, A.N. (1995) Candidate genes for the phycoerythrocyanin alpha subunit lyase. Biochemical analysis of pecE and pecF interposon mutants. J. Biol. Chem., 270, 12877-12884.
11. Storf, M., Parbel, A., Meyer, M., Strohmann, B., Scheer, H., Deng, M.G., Zheng, M., Zhou, M. and Zhao, K.H. (2001) Chromophore attachment to biliproteins: specificity of PecE/PecF, a lyase-isomerase for the photoactive 3(1)-cys-alpha 84-phycoviolobilin chromophore of phycoerythrocyanin. Biochemistry, 40, 12444-12456.
12. Zhao, K.H., Deng, M.G., Zheng, M., Zhou, M., Parbel, A., Storf, M., Meyer, M., Strohmann, B. and Scheer, H. (2000) Novel activity of a phycobiliprotein lyase: both the attachment of phycocyanobilin and the isomerization to phycoviolobilin are catalyzed by the proteins PecE and PecF encoded by the phycoerythrocyanin operon. FEBS Lett., 469, 9-13.
13. Zhao, K.H., Wu, D., Zhou, M., Zhang, L., Böhm, S., Bubenzer, C. and Scheer, H. (2005) Amino acid residues associated with enzymatic activities of the isomerizing phycoviolobilin-lyase PecE/ F. Biochemistry, 44, 8126-8137.
14. Sekar, S. and Chandramohan, M. (2008) Phycobiliproteins as a commodity: trends in applied research, patents and commercialization. J. Appl. Phycol., 20, 113-136.
15. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T.L. (2009) BLAST+: architecture and applications. BMC Bioinfo., 10, 421.
16. Coste, F. and Kerbellec, G. (2005) A similar fragments merging approach to learn Automata on proteins. In: Gama, J., Camacho, R., Brazdil, P., Jorge, A. and Torgo, L. (eds), Proceeding 16th European Conference on Machine Learning (ECML 2005). Springer-Verlag, Berlin, Heidelberg, Porto, Portugal, pp. 522-529.
17. Aravind, L. (2000) Guilt by association: contextual information in genome analysis. Genome Res., 10, 1074-1077.
18. Dolganov, N. and Grossman, A.R. (1999) A polypeptide with similarity to phycocyanin alpha-subunit phycocyanobilin lyase involved in degradation of phycobilisomes. J. Bacteriol., 181, 610-617.
19. Morimoto, K., Sato, S., Tabata, S. and Nakai, M. (2003) A HEAT-repeats containing protein, IaiH, stabilizes the iron-sulfur cluster bound to the cyanobacterial IscA homologue, IscA2. J. Biochem., 134, 211-217.
20. Rawlings, N.D., Morton, F.R., Kok, C.Y., Kong, J. and Barrett, A.J. (2008) MEROPS: the peptidase database. Nucleic Acids Res., 36, D320-D325.
21. Mulkidjanian, A.Y., Koonin, E.V., Makarova, K.S., Mekhedov, S.L., Sorokin, A., Wolf, Y.I., Dufresne, A., Partensky, F., Burd, H., Kaznadzey, D. et al. (2006) The cyanobacterial genome core and the origin of photosynthesis. Proc. Natl Acad. Sci. USA, 103, 13126-13131.
22. Kelley, L.A. and Sternberg, M.J. (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc., 4, 363-371.
23. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
24. Capella-Gutierrez, S., Silla-Martinez, J.M. and Gabaldon, T. (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972-1973.
25. Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W. and Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. System. Biol., 59, 307-321.
26. Zhao, K.H., Zhang, J., Tu, J.M., Bohm, S., Ploscher, M., Eichacker, L., Bubenzer, C., Scheer, H., Wang, X. and Zhou, M. (2007) Lyase activities of CpcS- and CpcT-like proteins from Nostoc PCC7120 and sequential reconstitution of binding sites of phycoerythrocyanin and phycocyanin beta-subunits. J. Biol. Chem., 282, 34093-34103.
27. Saunée, N.A., Williams, S.R., Bryant, D.A. and Schluchter, W.M. (2008) Biogenesis of phycobiliproteins: II. CpcS-I and CpcU comprise the heterodimeric bilin lyase that attaches phycocyanobilin to Cys-82 of beta-phycocyanin and Cys-81 of allophycocyanin subunits in Synechococcus sp. PCC 7002. J. Biol. Chem., 283, 7513-7522.