The Enzyme Database

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EC 1.3.7.2     
Accepted name: 15,16-dihydrobiliverdin:ferredoxin oxidoreductase
Reaction: 15,16-dihydrobiliverdin + oxidized ferredoxin = biliverdin IXα + reduced ferredoxin
For diagram of biliverdin metabolism, click here
Other name(s): PebA
Systematic name: 15,16-dihydrobiliverdin:ferredoxin oxidoreductase
Comments: Catalyses the two-electron reduction of biliverdin IXα at the C15 methine bridge. It has been proposed that this enzyme and EC 1.3.7.3, phycoerythrobilin:ferredoxin oxidoreductase, function as a dual enzyme complex in the conversion of biliverdin IXα into phycoerythrobilin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 347401-20-1
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]
[EC 1.3.7.2 created 2002]
 
 
EC 1.3.7.3     
Accepted name: phycoerythrobilin:ferredoxin oxidoreductase
Reaction: (3Z)-phycoerythrobilin + oxidized ferredoxin = 15,16-dihydrobiliverdin + reduced ferredoxin
For diagram of biliverdin metabolism, click here
Other name(s): PebB
Systematic name: (3Z)-phycoerythrobilin:ferredoxin oxidoreductase
Comments: Catalyses the two-electron reduction of the C2 and C31 diene system of 15,16-dihydrobiliverdin. Specific for 15,16-dihydrobiliverdin. It has been proposed that this enzyme and EC 1.3.7.2, 15,16-dihydrobiliverdin:ferredoxin oxidoreductase, function as a dual enzyme complex in the conversion of biliverdin IXα to phycoerythrobilin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 347401-21-2
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]
[EC 1.3.7.3 created 2002]
 
 
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 1.3.7.6     
Accepted name: phycoerythrobilin synthase
Reaction: (3Z)-phycoerythrobilin + 2 oxidized ferredoxin = biliverdin IXα + 2 reduced ferredoxin
Other name(s): PebS
Systematic name: (3Z)-phycoerythrobilin:ferredoxin oxidoreductase (from biliverdin IXα)
Comments: This enzyme, from a cyanophage infecting oceanic cyanobacteria of the Prochlorococcus genus, uses a four-electron reduction to carry out the reactions catalysed by EC 1.3.7.2 (15,16-dihydrobiliverdin:ferredoxin oxidoreductase) and EC 1.3.7.3 (phycoerythrobilin:ferredoxin oxidoreductase). 15,16-Dihydrobiliverdin is formed as a bound intermediate. Free 15,16-dihydrobiliverdin can also act as a substrate to form phycoerythrobilin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Dammeyer, T., Bagby, S.C., Sullivan, M.B., Chisholm, S.W. and Frankenberg-Dinkel, N. Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria. Curr. Biol. 18 (2008) 442–448. [DOI] [PMID: 18356052]
[EC 1.3.7.6 created 2008]
 
 
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 4.4.1.33     
Accepted name: R-phycocyanin α-cysteine-84 phycourobilin lyase/isomerase
Reaction: [R-phycocyanin α-subunit]-Cys84-phycourobilin = apo-[R-phycocyanin α-subunit] + (2R,3E)-phycoerythrobilin
Other name(s): rpcG (gene name)
Systematic name: [R-phycocyanin α-subunit]-Cys84-phycourobilin:(2R,3E)-phycoerythrobilin lyase/isomerase
Comments: The enzyme, characterized from the cyanobacterium Synechococcus sp. WH8102, catalyses the covalent attachment of the phycobilin chromophore phycoerythrobilin to cysteine 84 of the α subunit of the phycobiliprotein R-phycocyanin and its isomerization to phycourobilin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Blot, N., Wu, X.J., Thomas, J.C., Zhang, J., Garczarek, L., Bohm, S., Tu, J.M., Zhou, M., Ploscher, M., Eichacker, L., Partensky, F., Scheer, H. and Zhao, K.H. Phycourobilin in trichromatic phycocyanin from oceanic cyanobacteria is formed post-translationally by a phycoerythrobilin lyase-isomerase. J. Biol. Chem. 284 (2009) 9290–9298. [DOI] [PMID: 19182270]
[EC 4.4.1.33 created 2015]
 
 
EC 4.4.1.39     
Accepted name: C-phycoerythrin α-cysteine-82 phycoerythrobilin lyase
Reaction: a [C-phycoerythrin α-subunit]-Cys82-phycoerythrobilin = apo-[C-phycoerythrin α-subunit] + (3E)-phycoerythrobilin
Other name(s): cpeY (gene name)
Systematic name: [C-phycoerythrin α-subunit]-Cys82-phycoerythrobilin:phycoerythrobilin lyase
Comments: The enzyme, characterized from the cyanobacterium Microchaete diplosiphon, catalyses the attachment of the phycobilin chromophore (3E)-phycoerythrobilin (PEB) to cysteine 82 of the α subunit of the phycobiliprotein C-phycoerythrin. The numbering used here corresponds to the enzyme from Microchaete diplosiphon, and could vary slightly in other organisms. Activity is greatly enhanced in the presence of the chaperone-like protein CpeZ. The reaction could also be catalysed by EC 4.4.1.29, phycobiliprotein cysteine-84 phycobilin lyase, but much less efficiently.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Biswas, A., Boutaghou, M.N., Alvey, R.M., Kronfel, C.M., Cole, R.B., Bryant, D.A. and Schluchter, W.M. Characterization of the activities of the CpeY, CpeZ, and CpeS bilin lyases in phycoerythrin biosynthesis in Fremyella diplosiphon strain UTEX 481. J. Biol. Chem. 286 (2011) 35509–35521. [DOI] [PMID: 21865169]
2.  Kronfel, C.M., Biswas, A., Frick, J.P., Gutu, A., Blensdorf, T., Karty, J.A., Kehoe, D.M. and Schluchter, W.M. The roles of the chaperone-like protein CpeZ and the phycoerythrobilin lyase CpeY in phycoerythrin biogenesis. Biochim Biophys Acta Bioenerg 1860:S0005-2728( (2019). [DOI] [PMID: 31173730]
[EC 4.4.1.39 created 2021]
 
 
EC 4.4.1.40     
Accepted name: C-phycoerythrin β-cysteine-48/59 phycoerythrobilin lyase
Reaction: a [C-phycoerythrin β-subunit]-Cys48/59-phycoerythrobilin = apo-[C-phycoerythrin β-subunit] + (3E)-phycoerythrobilin
Other name(s): cpeF (gene name)
Systematic name: [C-phycoerythrin β-subunit]-Cys48/59-phycoerythrobilin:phycoerythrobilin lyase
Comments: The enzyme, characterized from the cyanobacterium Microchaete diplosiphon, catalyses the attachment of the phycobilin chromophore (3E)-phycoerythrobilin (PEB) to cysteine 48 and 59 of the β subunits of the phycobiliprotein C-phycoerythrin. The enzyme first ligates the A ring of PEB to cysteine-48, followed by the attachment of the D ring to cysteine-59. The numbering used here corresponds to the enzyme from Microchaete diplosiphon, and could vary slightly in other organisms. The reaction requires the presence of the chaperone-like protein CpeZ.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kronfel, C.M., Hernandez, C.V., Frick, J.P., Hernandez, L.S., Gutu, A., Karty, J.A., Boutaghou, M.N., Kehoe, D.M., Cole, R.B. and Schluchter, W.M. CpeF is the bilin lyase that ligates the doubly linked phycoerythrobilin on β-phycoerythrin in the cyanobacterium Fremyella diplosiphon. J. Biol. Chem. 294 (2019) 3987–3999. [DOI] [PMID: 30670589]
[EC 4.4.1.40 created 2021]
 
 


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