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Protochlorophyllide reductase

In enzymology, protochlorophyllide reductases (POR)[2][3] are enzymes that catalyze the conversion from protochlorophyllide to chlorophyllide a. They are oxidoreductases participating in the biosynthetic pathway to chlorophylls.[4][5]

The reduction of ring D of protochlorophyllide completes the biosynthesis of chlorophyllide a
light-dependent protochlorophyllide reductase
Identifiers
EC no.1.3.1.33
CAS no.68518-04-7
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light-independent protochlorophyllide reductase
Crystallographic structure of heterooctamer of a dark-operative protochlorophyllide oxidoreductase from Prochlorococcus marinus.[1]
Identifiers
EC no.1.3.7.7
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Search
PMCarticles
PubMedarticles
NCBIproteins

There are two structurally unrelated proteins with this sort of activity, referred to as light-dependent (LPOR) and dark-operative (DPOR). The light- and NADPH-dependent reductase is part of the short-chain dehydrogenase/reductase (SDR) superfamily and is found in plants and oxygenic photosynthetic bacteria,[6][7] while the ATP-dependent dark-operative version is a completely different protein, consisting of three subunits that exhibit significant sequence and quaternary structure similarity to the three subunits of nitrogenase.[8] This enzyme may be evolutionary older; due to its bound iron-sulfur clusters is highly sensitive to free oxygen and does not function if the atmospheric oxygen concentration exceeds about 3%.[9] It is possible that evolutionary pressure associated with the great oxidation event resulted in the development of the light-dependent system.

The light-dependent version (EC 1.3.1.33) uses NADPH:

protochlorophyllide NADPH H chlorophyllide a NADP

While the light-independent or dark-operative version (EC 1.3.7.7) uses ATP and ferredoxin:[10][11][12]

protochlorophyllide a reduced ferredoxin 2 ATP 2 H2O = chlorophyllide a oxidized ferredoxin 2 ADP 2 phosphate

Light-dependent

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The light-dependent version has the accepted name protochlorophyllide reductase. The systematic name is chlorophyllide-a :NADP 7,8-oxidoreductase. Other names in common use include NADPH2-protochlorophyllide oxidoreductase, NADPH-protochlorophyllide oxidoreductase, NADPH-protochlorophyllide reductase, protochlorophyllide oxidoreductase, and protochlorophyllide photooxidoreductase.

LPOR is one of only three known light-dependent enzymes. The enzyme enables light-dependent protochlorophyllide reduction via direct local hydride transfer from NADPH and a longer-range proton transfer along a defined structural pathway.[13] LPOR is a ~40kDa monomeric enzyme, for which the structure has been solved by X-ray crystallography. It is part of the SDR superfamily, which includes alcohol dehydrogenase, and consists of a Rossman-fold NADPH-binding site and a substrate-specific C-terminal segment region. The protochlorophyllide substrate is thought to bind to a cavity near the nicotinamide end of the bound NADPH.[7][13] LPOR is primarily found in plants and oxygenic photosynthetic bacteria, as well as in some algae.

Light-independent

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The light-independent version has the accepted name of ferredoxin:protochlorophyllide reductase (ATP-dependent). Systematically it is known as ATP-dependent ferredoxin:protochlorophyllide-a 7,8-oxidoreductase. Other names in common use include light-independent protochlorophyllide reductase and dark-operative protochlorophyllide reductase (DPOR).

DPOR is a nitrogenase homologue[8] and adopts an almost identical overall architecture arrangement to both nitrogenase as well as the downstream chlorophyllide a reductase (COR). The enzyme consists of a catalytic heterotetramer and two transiently-bound ATPase dimers (right).[14] Similar to nitrogenase, the reduction mechanism relies on an electron transfer from the iron-sulfur cluster of the ATPase domain, through a secondary cluster on the catalytic heterotetramer and finally to the protochlorophyllide-bound active site (which, distinct from nitrogenase, does not contain FeMoco). The reduction requires significantly less input than the nitrogenase reaction, requiring only a 2-electron reduction and 4 ATP equivalents, and as such may require an auto-inhibitory mechanism to avoid over-activity.[15]

DPOR can alternatively take as its substrate the compound with a second vinyl group (instead of an ethyl group) in the structure, in which case the reaction is

3,8-divinylprotochlorophyllide reduced ferredoxin 2 ATP 2 H2O   3,8-divinylchlorophyllide a oxidized ferredoxin 2 ADP 2 phosphate

This enzyme is present in photosynthetic bacteria, cyanobacteria, green algae and gymnosperms.[4][16]

See also

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References

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  1. ^ PDB: 2ynm​; Moser J, Lange C, Krausze J, Rebelein J, Schubert WD, Ribbe MW, Heinz DW, Jahn D (2013). "Structure of ADP-aluminium fluoride-stabilized protochlorophyllide oxidoreductase complex". Proc Natl Acad Sci U S A. 110 (6): 2094–2098. Bibcode:2013PNAS..110.2094M. doi:10.1073/pnas.1218303110. PMC 3568340. PMID 23341615.2094-2098&rft.date=2013&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568340#id-name=PMC&rft_id=info:pmid/23341615&rft_id=info:doi/10.1073/pnas.1218303110&rft_id=info:bibcode/2013PNAS..110.2094M&rft.aulast=Moser&rft.aufirst=J&rft.au=Lange, C&rft.au=Krausze, J&rft.au=Rebelein, J&rft.au=Schubert, WD&rft.au=Ribbe, MW&rft.au=Heinz, DW&rft.au=Jahn, D&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568340&rfr_id=info:sid/en.wikipedia.org:Protochlorophyllide reductase" class="Z3988">
  2. ^ Griffiths WT (1978). "Reconstitution of chlorophyllide formation by isolated etioplast membranes". Biochem. J. 174 (3): 681–92. doi:10.1042/bj1740681. PMC 1185970. PMID 31865.681-92&rft.date=1978&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1185970#id-name=PMC&rft_id=info:pmid/31865&rft_id=info:doi/10.1042/bj1740681&rft.au=Griffiths WT&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1185970&rfr_id=info:sid/en.wikipedia.org:Protochlorophyllide reductase" class="Z3988">
  3. ^ Apel K, Santel HJ, Redlinger TE, Falk H (1980). "The protochlorophyllide holochrome of barley (Hordeum vulgare L.) Isolation and characterization of the NADPH:protochlorophyllide oxidoreductase". Eur. J. Biochem. 111 (1): 251–8. doi:10.1111/j.1432-1033.1980.tb06100.x. PMID 7439188.251-8&rft.date=1980&rft_id=info:doi/10.1111/j.1432-1033.1980.tb06100.x&rft_id=info:pmid/7439188&rft.aulast=Apel&rft.aufirst=K&rft.au=Santel, HJ&rft.au=Redlinger, TE&rft.au=Falk, H&rft_id=https://doi.org/10.1111%2Fj.1432-1033.1980.tb06100.x&rfr_id=info:sid/en.wikipedia.org:Protochlorophyllide reductase" class="Z3988">
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  5. ^ Bollivar, David W. (2007). "Recent advances in chlorophyll biosynthesis". Photosynthesis Research. 90 (2): 173–194. doi:10.1007/s11120-006-9076-6. PMID 17370354. S2CID 23808539.173-194&rft.date=2007&rft_id=https://api.semanticscholar.org/CorpusID:23808539#id-name=S2CID&rft_id=info:pmid/17370354&rft_id=info:doi/10.1007/s11120-006-9076-6&rft.aulast=Bollivar&rft.aufirst=David W.&rfr_id=info:sid/en.wikipedia.org:Protochlorophyllide reductase" class="Z3988">
  6. ^ Nomata, Jiro; Kondo, Toru; Mizoguchi, Tadashi; Tamiaki, Hitoshi; Itoh, Shigeru; Fujita, Yuichi (May 2015). "Dark-operative protochlorophyllide oxidoreductase generates substrate radicals by an iron-sulphur cluster in bacteriochlorophyll biosynthesis". Scientific Reports. 4 (1): 5455. doi:10.1038/srep05455. ISSN 2045-2322. PMC 4071322. PMID 24965831.
  7. ^ a b Dong, Chen-Song; Zhang, Wei-Lun; Wang, Qiao; Li, Yu-Shuai; Wang, Xiao; Zhang, Min; Liu, Lin (2020-04-14). "Crystal structures of cyanobacterial light-dependent protochlorophyllide oxidoreductase". Proceedings of the National Academy of Sciences. 117 (15): 8455–8461. doi:10.1073/pnas.1920244117. ISSN 0027-8424. PMC 7165480. PMID 32234783.8455-8461&rft.date=2020-04-14&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165480#id-name=PMC&rft.issn=0027-8424&rft_id=info:pmid/32234783&rft_id=info:doi/10.1073/pnas.1920244117&rft.aulast=Dong&rft.aufirst=Chen-Song&rft.au=Zhang, Wei-Lun&rft.au=Wang, Qiao&rft.au=Li, Yu-Shuai&rft.au=Wang, Xiao&rft.au=Zhang, Min&rft.au=Liu, Lin&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165480&rfr_id=info:sid/en.wikipedia.org:Protochlorophyllide reductase" class="Z3988">
  8. ^ a b Yuichi Fujita and Carl E. Bauer (2000). Reconstitution of Light-independent Protochlorophyllide Reductase from Purified Bchl and BchN-BchB Subunits. J. Biol. Chem., Vol. 275, Issue 31, 23583-23588. [1]
  9. ^ S.Yamazaki, J.Nomata, Y.Fujita (2006) Differential operation of dual protochlorophyllide reductases for chlorophyll biosynthesis in response to environmental oxygen levels in the cyanobacterium Leptolyngbya boryana. Plant Physiology, 2006, 142, 911-922 [2]
  10. ^ Fujita Y, Matsumoto H, Takahashi Y, Matsubara H (March 1993). "Identification of a nifDK-like gene (ORF467) involved in the biosynthesis of chlorophyll in the cyanobacterium Plectonema boryanum". Plant & Cell Physiology. 34 (2): 305–14. PMID 8199775.305-14&rft.date=1993-03&rft_id=info:pmid/8199775&rft.aulast=Fujita&rft.aufirst=Y&rft.au=Matsumoto, H&rft.au=Takahashi, Y&rft.au=Matsubara, H&rfr_id=info:sid/en.wikipedia.org:Protochlorophyllide reductase" class="Z3988">
  11. ^ Nomata J, Ogawa T, Kitashima M, Inoue K, Fujita Y (April 2008). "NB-protein (BchN-BchB) of dark-operative protochlorophyllide reductase is the catalytic component containing oxygen-tolerant Fe-S clusters". FEBS Letters. 582 (9): 1346–50. doi:10.1016/j.febslet.2008.03.018. PMID 18358835.1346-50&rft.date=2008-04&rft_id=info:doi/10.1016/j.febslet.2008.03.018&rft_id=info:pmid/18358835&rft.aulast=Nomata&rft.aufirst=J&rft.au=Ogawa, T&rft.au=Kitashima, M&rft.au=Inoue, K&rft.au=Fujita, Y&rft_id=https://doi.org/10.1016%2Fj.febslet.2008.03.018&rfr_id=info:sid/en.wikipedia.org:Protochlorophyllide reductase" class="Z3988">
  12. ^ Muraki N, Nomata J, Ebata K, Mizoguchi T, Shiba T, Tamiaki H, et al. (May 2010). "X-ray crystal structure of the light-independent protochlorophyllide reductase". Nature. 465 (7294): 110–4. Bibcode:2010Natur.465..110M. doi:10.1038/nature08950. PMID 20400946. S2CID 4427639.110-4&rft.date=2010-05&rft_id=info:doi/10.1038/nature08950&rft_id=https://api.semanticscholar.org/CorpusID:4427639#id-name=S2CID&rft_id=info:pmid/20400946&rft_id=info:bibcode/2010Natur.465..110M&rft.aulast=Muraki&rft.aufirst=N&rft.au=Nomata, J&rft.au=Ebata, K&rft.au=Mizoguchi, T&rft.au=Shiba, T&rft.au=Tamiaki, H&rft.au=Kurisu, G&rft.au=Fujita, Y&rfr_id=info:sid/en.wikipedia.org:Protochlorophyllide reductase" class="Z3988">
  13. ^ a b Zhang, Shaowei; Heyes, Derren J.; Feng, Lingling; Sun, Wenli; Johannissen, Linus O.; Liu, Huanting; Levy, Colin W.; Li, Xuemei; Yang, Ji; Yu, Xiaolan; Lin, Min (2019-10-31). "Structural basis for enzymatic photocatalysis in chlorophyll biosynthesis". Nature. 574 (7780): 722–725. Bibcode:2019Natur.574..722Z. doi:10.1038/s41586-019-1685-2. ISSN 0028-0836. PMID 31645759. S2CID 204849396.722-725&rft.date=2019-10-31&rft_id=https://api.semanticscholar.org/CorpusID:204849396#id-name=S2CID&rft_id=info:bibcode/2019Natur.574..722Z&rft.issn=0028-0836&rft_id=info:doi/10.1038/s41586-019-1685-2&rft_id=info:pmid/31645759&rft.aulast=Zhang&rft.aufirst=Shaowei&rft.au=Heyes, Derren J.&rft.au=Feng, Lingling&rft.au=Sun, Wenli&rft.au=Johannissen, Linus O.&rft.au=Liu, Huanting&rft.au=Levy, Colin W.&rft.au=Li, Xuemei&rft.au=Yang, Ji&rft.au=Yu, Xiaolan&rft.au=Lin, Min&rft_id=http://www.nature.com/articles/s41586-019-1685-2&rfr_id=info:sid/en.wikipedia.org:Protochlorophyllide reductase" class="Z3988">
  14. ^ Moser, Jürgen; Lange, Christiane; Krausze, Joern; Rebelein, Johannes; Schubert, Wolf-Dieter; Ribbe, Markus W.; Heinz, Dirk W.; Jahn, Dieter (2013-02-05). "Structure of ADP-aluminium fluoride-stabilized protochlorophyllide oxidoreductase complex". Proceedings of the National Academy of Sciences. 110 (6): 2094–2098. Bibcode:2013PNAS..110.2094M. doi:10.1073/pnas.1218303110. ISSN 0027-8424. PMC 3568340. PMID 23341615.2094-2098&rft.date=2013-02-05&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568340#id-name=PMC&rft_id=info:bibcode/2013PNAS..110.2094M&rft_id=info:pmid/23341615&rft_id=info:doi/10.1073/pnas.1218303110&rft.issn=0027-8424&rft.aulast=Moser&rft.aufirst=Jürgen&rft.au=Lange, Christiane&rft.au=Krausze, Joern&rft.au=Rebelein, Johannes&rft.au=Schubert, Wolf-Dieter&rft.au=Ribbe, Markus W.&rft.au=Heinz, Dirk W.&rft.au=Jahn, Dieter&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568340&rfr_id=info:sid/en.wikipedia.org:Protochlorophyllide reductase" class="Z3988">
  15. ^ Corless, Elliot I.; Saad Imran, Syed Muhammad; Watkins, Maxwell B.; Bacik, John-Paul; Mattice, Jenna R.; Patterson, Angela; Danyal, Karamatullah; Soffe, Mark; Kitelinger, Robert; Seefeldt, Lance C.; Origanti, Sofia (January 2021). "The flexible N-terminus of BchL autoinhibits activity through interaction with its [4Fe-4S] cluster and released upon ATP binding". Journal of Biological Chemistry. 296: 100107. doi:10.1074/jbc.RA120.016278. PMC 7948495. PMID 33219127.
  16. ^ Bollivar DW (November 2006). "Recent advances in chlorophyll biosynthesis". Photosynthesis Research. 90 (2): 173–94. doi:10.1007/s11120-006-9076-6. PMID 17370354. S2CID 23808539.173-94&rft.date=2006-11&rft_id=https://api.semanticscholar.org/CorpusID:23808539#id-name=S2CID&rft_id=info:pmid/17370354&rft_id=info:doi/10.1007/s11120-006-9076-6&rft.aulast=Bollivar&rft.aufirst=DW&rfr_id=info:sid/en.wikipedia.org:Protochlorophyllide reductase" class="Z3988">

Ferredoxin:protochlorophyllide reductase (ATP-dependent) at the U.S. National Library of Medicine Medical Subject Headings (MeSH)

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