The Enzyme Database

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EC 1.3.7.5     
Accepted name: phycocyanobilin:ferredoxin oxidoreductase
Reaction: (3Z)-phycocyanobilin + 4 oxidized ferredoxin = biliverdin IXα + 4 reduced ferredoxin
For diagram of biliverdin metabolism, click here
Systematic name: (3Z)-phycocyanobilin:ferredoxin oxidoreductase
Comments: Catalyses the four-electron reduction of biliverdin IXα (2-electron reduction at both the A and D rings). Reaction proceeds via an isolatable 2-electron intermediate, 181,182-dihydrobiliverdin. Flavodoxins can be used instead of ferredoxin. The direct conversion of biliverdin IXα (BV) to (3Z)-phycocyanolbilin (PCB) in the cyanobacteria Synechocystis sp. PCC 6803, Anabaena sp. PCC7120 and Nostoc punctiforme is in contrast to the proposed pathways of PCB biosynthesis in the red alga Cyanidium caldarium, which involves (3Z)-phycoerythrobilin (PEB) as an intermediate [2] and in the green alga Mesotaenium caldariorum, in which PCB is an isolable intermediate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 347401-12-1
References:
1.  Frankenberg, N., Mukougawa, K., Kohchi, T. and Lagarias, J.C. Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms. Plant Cell 13 (2001) 965–978. [PMID: 11283349]
2.  Beale, S.I. Biosynthesis of phycobilins. Chem. Rev. 93 (1993) 785–802.
3.  Wu, S.-H., McDowell, M.T. and Lagarias, J.C. Phycocyanobilin is the natural chromophore precursor of phytochrome from the green alga Mesotaenium caldariorum. J. Biol. Chem. 272 (1997) 25700–25705. [DOI] [PMID: 9325294]
[EC 1.3.7.5 created 2002, modified 2014]
 
 
EC 4.4.1.29     
Accepted name: phycobiliprotein cysteine-84 phycobilin lyase
Reaction: (1) [C-phycocyanin β-subunit]-Cys84-phycocyanobilin = apo-[C-phycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(2) [phycoerythrocyanin β-subunit]-Cys84-phycocyanobilin = apo-[phycoerythrocyanin β-subunit] + (2R,3E)-phycocyanobilin
(3) [allophycocyanin α-subunit]-Cys84-phycocyanobilin = apo-[allophycocyanin α-subunit] + (2R,3E)-phycocyanobilin
(4) [allophycocyanin β-subunit]-Cys84-phycocyanobilin = apo-[allophycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(5) [C-phycoerythrin α-subunit]-Cys84-phycoerythrobilin = apo-[C-phycoerythrin α-subunit] + (2R,3E)-phycoerythrobilin
(6) [C-phycoerythrin β-subunit]-Cys84-phycoerythrobilin = apo-[C-phycoerythrin β-subunit] + (2R,3E)-phycoerythrobilin
Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin
phycoerythrobilin = 3,31,181,182-tetradehydro-2,3,15,16-tetrahydromesobiliverdin
Other name(s): cpcS (gene name); cpeS (gene name); cpcS1 (gene name); cpcU (gene name); phycocyanobilin:Cys-β84-phycobiliprotein lyase
Systematic name: [phycobiliprotein]-Cys84-phycobilin:phycobilin lyase
Comments: The enzyme, found in cyanobacteria and red algae, catalyses the attachment of phycobilin chromophores to cysteine 84 of several phycobiliproteins (the numbering used here corresponds to the enzyme from Anabaena, in other organisms the number may vary slightly). It can attach phycocyanobilin to the β subunits of C-phycocyanin and phycoerythrocyanin and to both subunits of allophycocyanin. In addition, it can attach phycoerythrobilin to both subunits of C-phycoerythrin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zhao, K.H., Su, P., Li, J., Tu, J.M., Zhou, M., Bubenzer, C. and Scheer, H. Chromophore attachment to phycobiliprotein β-subunits: phycocyanobilin:cysteine-β84 phycobiliprotein lyase activity of CpeS-like protein from Anabaena Sp. PCC7120. J. Biol. Chem. 281 (2006) 8573–8581. [DOI] [PMID: 16452471]
2.  Zhao, K.H., Su, P., Tu, J.M., Wang, X., Liu, H., Ploscher, M., Eichacker, L., Yang, B., Zhou, M. and Scheer, H. Phycobilin:cystein-84 biliprotein lyase, a near-universal lyase for cysteine-84-binding sites in cyanobacterial phycobiliproteins. Proc. Natl. Acad. Sci. USA 104 (2007) 14300–14305. [DOI] [PMID: 17726096]
3.  Saunee, N.A., Williams, S.R., Bryant, D.A. and Schluchter, W.M. Biogenesis of phycobiliproteins: II. CpcS-I and CpcU comprise the heterodimeric bilin lyase that attaches phycocyanobilin to Cys-82 of β-phycocyanin and Cys-81 of allophycocyanin subunits in Synechococcus sp. PCC 7002. J. Biol. Chem. 283 (2008) 7513–7522. [DOI] [PMID: 18199753]
4.  Kupka, M., Zhang, J., Fu, W.L., Tu, J.M., Bohm, S., Su, P., Chen, Y., Zhou, M., Scheer, H. and Zhao, K.H. Catalytic mechanism of S-type phycobiliprotein lyase: chaperone-like action and functional amino acid residues. J. Biol. Chem. 284 (2009) 36405–36414. [DOI] [PMID: 19864423]
[EC 4.4.1.29 created 2015]
 
 
EC 4.4.1.30     
Accepted name: phycobiliprotein β-cysteine-155 phycobilin lyase
Reaction: (1) [C-phycocyanin β-subunit]-Cys155-phycocyanobilin = apo-[C-phycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(2) [phycoerythrocyanin β-subunit]-Cys155-phycocyanobilin = apo-[phycoerythrocyanin β-subunit] + (2R,3E)-phycocyanobilin
Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin
Other name(s): cpcT (gene name); cpeT1 (gene name); cpcT1 (gene name)
Systematic name: [phycobiliprotein β-subunit]-Cys155-phycocyanobilin:phycocyanobilin lyase
Comments: The enzyme, found in cyanobacteria and red algae, catalyses the attachment of the phycobilin chromophore phycocyanobilin to cysteine 155 of the β subunits of the phycobiliproteins C-phycocyanin and phycoerythrocyanin. The numbering used here corresponds to the enzyme from Anabaena, and could vary slightly in other organisms.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zhao, K.H., Zhang, J., Tu, J.M., Bohm, S., Ploscher, M., Eichacker, L., Bubenzer, C., Scheer, H., Wang, X. and Zhou, M. Lyase activities of CpcS- and CpcT-like proteins from Nostoc PCC7120 and sequential reconstitution of binding sites of phycoerythrocyanin and phycocyanin β-subunits. J. Biol. Chem. 282 (2007) 34093–34103. [DOI] [PMID: 17895251]
2.  Zhang, R., Feng, X.T., Wu, F., Ding, Y., Zang, X.N., Zhang, X.C., Yuan, D.Y. and Zhao, B.R. Molecular cloning and expression analysis of a new bilin lyase: the cpcT gene encoding a bilin lyase responsible for attachment of phycocyanobilin to Cys-153 on the β-subunit of phycocyanin in Arthrospira platensis FACHB314. Gene 544 (2014) 191–197. [DOI] [PMID: 24768724]
3.  Zhou, W., Ding, W.L., Zeng, X.L., Dong, L.L., Zhao, B., Zhou, M., Scheer, H., Zhao, K.H. and Yang, X. Structure and mechanism of the phycobiliprotein lyase CpcT. J. Biol. Chem. 289 (2014) 26677–26689. [DOI] [PMID: 25074932]
[EC 4.4.1.30 created 2015]
 
 
EC 4.4.1.31     
Accepted name: phycoerythrocyanin α-cysteine-84 phycoviolobilin lyase/isomerase
Reaction: [phycoerythrocyanin α-subunit]-Cys84-phycoviolobilin = apo-[phycoerythrocyanin α-subunit] + (2R,3E)-phycocyanobilin
Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin
phycoviolobilin = 15,16-dihydrobiliverdin IIIa
Other name(s): pecE (gene name); pecF (gene name); phycoviolobilin phycoerythrocyanin-α84-cystein-lyase; PecE/PecF; PEC-Cys-R84 PCB lyase/isomerase
Systematic name: [phycoerythrocyanin α-subunit]-Cys84-phycoviolobilin:(2R,3E)-phycocyanobilin lyase/isomerase
Comments: The enzyme, characterized from the cyanobacteria Nostoc sp. PCC 7120 and Mastigocladus laminosus, catalyses the covalent attachment of the phycobilin chromophore phycocyanobilin to cysteine 84 of the β subunit of the phycobiliprotein phycoerythrocyanin and its isomerization to phycoviolobilin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Jung, L.J., Chan, C.F. and Glazer, A.N. Candidate genes for the phycoerythrocyanin α subunit lyase. Biochemical analysis of pecE and pecF interposon mutants. J. Biol. Chem. 270 (1995) 12877–12884. [DOI] [PMID: 7759546]
2.  Zhao, K.H., Deng, M.G., Zheng, M., Zhou, M., Parbel, A., Storf, M., Meyer, M., Strohmann, B. and Scheer, H. 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 (2000) 9–13. [DOI] [PMID: 10708746]
3.  Storf, M., Parbel, A., Meyer, M., Strohmann, B., Scheer, H., Deng, M.G., Zheng, M., Zhou, M. and Zhao, K.H. Chromophore attachment to biliproteins: specificity of PecE/PecF, a lyase-isomerase for the photoactive 31-cys-α 84-phycoviolobilin chromophore of phycoerythrocyanin. Biochemistry 40 (2001) 12444–12456. [DOI] [PMID: 11591166]
4.  Zhao, K.H., Wu, D., Wang, L., Zhou, M., Storf, M., Bubenzer, C., Strohmann, B. and Scheer, H. Characterization of phycoviolobilin phycoerythrocyanin-α 84-cystein-lyase-(isomerizing) from Mastigocladus laminosus. Eur. J. Biochem. 269 (2002) 4542–4550. [DOI] [PMID: 12230566]
[EC 4.4.1.31 created 2015]
 
 
EC 4.4.1.32     
Accepted name: C-phycocyanin α-cysteine-84 phycocyanobilin lyase
Reaction: [C-phycocyanin α-subunit]-Cys84-phycocyanobilin = apo-[C-phycocyanin α-subunit] + (2R,3E)-phycocyanobilin
Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin
Other name(s): cpcE (gene name); cpcF (gene name)
Systematic name: [C-phycocyanin α-subunit]-Cys84-phycocyanobilin:(2R,3E)-phycocyanobilin lyase
Comments: The enzyme, characterized from the cyanobacterium Synechococcus elongatus PCC 7942, catalyses the covalent attachment of the phycobilin chromophore phycocyanobilin to cysteine 84 of the α subunit of the phycobiliprotein C-phycocyanin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Fairchild, C.D., Zhao, J., Zhou, J., Colson, S.E., Bryant, D.A. and Glazer, A.N. Phycocyanin α-subunit phycocyanobilin lyase. Proc. Natl. Acad. Sci. USA 89 (1992) 7017–7021. [DOI] [PMID: 1495995]
2.  Fairchild, C.D. and Glazer, A.N. Oligomeric structure, enzyme kinetics, and substrate specificity of the phycocyanin α subunit phycocyanobilin lyase. J. Biol. Chem. 269 (1994) 8686–8694. [PMID: 8132596]
3.  Bhalerao, R.P., Lind, L.K. and Gustafsson, P. Cloning of the cpcE and cpcF genes from Synechococcus sp. PCC 6301 and their inactivation in Synechococcus sp. PCC 7942. Plant Mol. Biol. 26 (1994) 313–326. [PMID: 7524727]
[EC 4.4.1.32 created 2015]
 
 


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