Skip to main content
Log in

Structure and Function of Plant-Type Ferredoxins

  • Published:
Photosynthesis Research Aims and scope Submit manuscript

Abstract

The plant-type ferredoxins (Fds) are the [2Fe–2S] proteins that function primarily in photosynthesis; they transfer electrons from photoreduced Photosystem I to ferredoxin NADP+ reductase in which NADPH is produced for CO2 assimilation. In addition, Fds partition electrons to various ferredoxin-dependent enzymes not only for assimilations of inorganic nitrogen and sulfur and N2 fixation but also for regulation of CO2 assimilation cycle. Although Fds are small iron–sulfur proteins with molecular weight of 11 KDa, they are expected to interact with surprisingly many enzymes. Several Fd isoforms were found in non-photosynthetic cells as well as Fds in photosynthetic cells, leading to the recognition that they have differentiated physiological roles. In a quarter of century, X-ray crystallography and NMR spectroscopy provided wealth of structural data, which shed light on the structure–function relationship of the plant-type Fds and gave structural basis for the biochemical and spectroscopic properties so far accumulated. Thus the structural studies of Fds have come to a new era in which different roles of Fds and interactions with various enzymes are clarified on the basis of the tertiary and quaternary structures, although they are premature at present. This article reviews briefly the structures of the plant-type Fds together with their functions, properties, and interactions with Fd related enzymes. Lastly the folding motif of Fd, that has grown to be a large family by including many functionally unrelated proteins, is noted.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Akashi T, Matsumura T, Ideguchi T, Iwakiri K, Kawakatsu T, Taniguchi I and Hase T (1999) Comparison of the electrostatic binding sites on the surface of ferredoxin for two ferredoxin-dependent enzymes, ferredoxin-NADP+ reductase and sulfite reductase. J Biol Chem 274: 29399–29405

    Article  PubMed  CAS  Google Scholar 

  • Arnon DI (1965) Ferredoxin and photosynthesis. Science 149: 1460–1470

    PubMed  CAS  Google Scholar 

  • Arnon DI (1988) The discovery of ferredoxin: the photosynthetic path. Trends Biochem Sci 13: 30–33

    Article  PubMed  CAS  Google Scholar 

  • Banci L, Bertini I and Luchinat C (1990) The 1H NMR parameters of magnetically coupled dimers: The Fe2S2 proteins as an example. Struct Bonding 72: 113–136

    CAS  Google Scholar 

  • Bes MT, Parisini E, Inda LA, Saraiva LM, Peleato ML and Sheldrick GM (1999) Crystal structure determination at 1.4 Å resolution of ferredoxin from the green alga Chlorella fusca. Structure 7: 1201–1211

    Article  PubMed  CAS  Google Scholar 

  • Binda C, Coda A, Aliverti A, Zanetti G and Mattevi A (1998) Structure of the mutant E92K of [2Fe-2S] ferredoxin I from Spinacia oleracea at 1.7 Åresolution. Acta Crystallogr D54: 1353–1358

    CAS  Google Scholar 

  • Böhme H and Schrautemeier B (1987) Electron donation to nitrogenase in a cell-free system from heterocyst Anabaena variabilis. Biochim Biophys Acta 891: 115–120

    Article  Google Scholar 

  • Bruschi M and Guerlesquin F (1988) Structure, function and evolution of bacterial ferredoxins. FEMS Microbiol Rev 54: 155–176

    Article  CAS  Google Scholar 

  • Buchanan BB (1980) Role of light in the regulation of chloroplast enzymes. Annu Rev Plant Physiol 31: 341–374

    Article  CAS  Google Scholar 

  • Cammack R, Rao KK, Bargeron CP, Hutson KG, Andrew PW and Rogers LJ (1977) Midpoint redox potentials of plant and algal ferredoxins. Biochem J 168: 205–209

    PubMed  CAS  Google Scholar 

  • Correl CC, Batie CJ, Ballou DP and Ludwig ML (1992) Phthalate dioxygenase reductase: a molecular structure for electron transfer from pyridine nucleotide to [2Fe-2S]. Science 258: 1604–1610

    Google Scholar 

  • Crossnoe CR, Germanas JP, LeMagueres P, Mustata G and Krause KL (2002) The crystal structure of Trichomonas vaginalis ferredoxin provides insight into metronidazole activation. J Mol Biol 318: 503–518

    Article  PubMed  CAS  Google Scholar 

  • De Pascalis AR, Jelesarov I, Ackermann F, Koppenol WH, Hirasawa M, Knaff DB and Bosshard HR (1993) Binding of ferredoxin to ferredoxin:NADP+ oxidoreductase: the role of carboxyl groups, electrostatic surface potential, and molecular dipole moment. Prot Sci 2: 1126–1135

    CAS  Google Scholar 

  • Dunham WR, Bearden AJ, Salmeen IT, Palmer G, Sands RH, Orme-Johnson WH and Beinert H (1971) The two-iron ferredoxins in spinach, parsley, pig adrenal cortex, Azotobacter vinelandii,, and Clostridium pasteurianum: studies by magnetic field Mossbauer spectroscopy. Biochim Biophys Acta 253: 134–152

    Article  PubMed  CAS  Google Scholar 

  • Enroth C, Eger BT, Okamoto K, Nishino T, Nishino T and Pai EF (2000) Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: structure-based mechanism of conversion. Proc Natl Acad Sci USA 97: 10723–10728

    Article  PubMed  CAS  Google Scholar 

  • Foust GP, Mayhew SG and Massey V (1969) Complex formation between ferredoxin triphosphopyridine nucleotide reductase and electron transfer proteins. J Biol Chem 244: 964–970

    Google Scholar 

  • Frolow F, Harel M, Sussman JL, Mevarech M and Shoham M (1996) Insights into protein adaptation to a saturated salt environment from the crystal structure of halophilic 2Fe-2S ferredoxin. Nat Struct Biol 3: 452–458

    Article  PubMed  CAS  Google Scholar 

  • Fukuyama K (2001) Ferredoxins containing one [4Fe-4S] center. In: Messerschmidt A, Huber R, Poulos T and Wieghardt K (eds) Handbook of Metalloproteins, pp 543–552. John Wiley & Sons, UK

    Google Scholar 

  • Fukuyama K, Hase T, Matsumoto S, Tsukihara T, Katsube Y, Tanaka N, Kakudo M, Wada K and Matsubara H (1980) Structure of S. platensis [2Fe-2S] ferredoxin and evolution of chloroplast-type ferredoxins. Nature 286: 522–524

    Article  CAS  Google Scholar 

  • Fukuyama K, Nagahara Y, Tsukihara T, Katsube Y, Hase T and Matsubara H (1988) Tertiary structure of Bacillus thermoproteolyticus [4Fe-4S] ferredoxin: evolutionary implications for bacterial ferredoxins. J Mol Biol 199: 183–193

    Article  PubMed  CAS  Google Scholar 

  • Fukuyama K, Ueki N, Nakamura H, Tsukihara T and Matsubara H (1995) Tertiary structure of [2Fe-2S] ferredoxin from Spirulina platensis refined at 2.5 Åresolution: structural comparisons of plant-type ferredoxins and an electrostatic potential analysis. J Biochem 117: 1017–1023

    PubMed  CAS  Google Scholar 

  • Hanke GT, Kimata-Ariga Y, Taniguchi I and Hase T (2004) A post genomic characterization of arabidopsis ferredoxins. Plant Physiol 134: 255–264

    Article  PubMed  CAS  Google Scholar 

  • Hänzelmann P, Dobbek H, Gremer L, Huber R and Meyer O (2000) The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur falvoenzyme carbon monoxide dehydrogenase. J Mol Biol 301: 1221–1235

    Article  PubMed  CAS  Google Scholar 

  • Hase T, Kimata Y, Yonekura K, Matsumura T and Sakakibara H (1991) Molecular cloning and differential expression of the maize ferredoxin gene family. Plant Physiol 96: 77–83

    PubMed  CAS  Google Scholar 

  • Hanke GT, Kurisu G, Kusunoki M and Hase T (2004) Fd: FNR electron transfer complexes: evolutionary refinement of structural interactions. Photosynth Res 81: 317–327 (this issue)

    Article  PubMed  CAS  Google Scholar 

  • Hatanaka H, Tanimura R, Katoh S and Inagaki F (1997) Solution structure of ferredoxin from thermophilic cyanobacterium Synechococcus elongatus and its thermostability. J Mol Biol 268: 922–933

    Article  PubMed  CAS  Google Scholar 

  • Holden HM, Jacobson BL, Hurley JK, Tollin G, Oh B-H, Skjeldal L, Chae YK, Cheng H, Xia B and Markley JL (1994) Structure-function studies of [2Fe-2S] ferredoxins. J Bioenerg Biomemb 26: 67–88

    Article  CAS  Google Scholar 

  • Hurley JK, Cheng H, Xia B, Markley JL, Medina M, Gomez-Moreno C and Tollin G (1993) An aromatic amino acid is required at position 65 in Anabaena ferredoxin for rapid electron transfer to ferredoxin: NADP+ reductase. J Am Chem Soc 115: 11698–11701

    Article  CAS  Google Scholar 

  • Hurley JK, Weber-Main AM, Hodges AE, Stankovich MT, Benning MM, Holden HM, Cheng H, Xia B, Markley JL, Genzor C, Gomez-Moreno C, Hafezi R and Tollin G (1997) Iron-sulfur cluster cysteine-to-serine mutants of Anahaena [2Fe-2S] ferredoxin exhibit unexpected redox properties and are competent in electron transfer to ferredoxin:NADP+ reductase. Biochemistry 36: 15109–15117

    Article  PubMed  CAS  Google Scholar 

  • Ikemizu S, Bando M, Sato T, Morimoto Y, Tsukihara T and Fukuyama K (1994) Structure of [2Fe-2S] Ferredoxin I from Equisetum arvense at 1.8 Åresolution. Acta Crystallogr D 50: 167–174

    CAS  Google Scholar 

  • Im S-C, Liu G, Luchinat C, Sykes G and Bertini I (1998) The solution structure of parsley [2Fe-2S] ferredoxin. Eur J Biochem 258: 465–477

    Article  PubMed  CAS  Google Scholar 

  • Iverson TM, Luna-Chavez C, Cecchini G and Rees DC (1999) Structure of the Echerichia coli fumarate reductase respiratory complex. Science 284: 1961–1966

    Article  PubMed  CAS  Google Scholar 

  • Jacobson BL, Chae YK, Markley JL, Rayment I and Holden HM (1993) Molecular structure of the oxidized, recombinant, heterocyst [2Fe-2S] ferredoxin from Anabaena 7120 determined to 1.7-Åresolution. Biochemistry 32: 6788–6793

    Article  PubMed  CAS  Google Scholar 

  • Johnston SC, Riddle SM, Cohen RE and Hill CP (1999) Structural basis for the specificity of ubuquitin C-terminal hydrolases. EMBO J 18: 3877–3887

    Article  PubMed  CAS  Google Scholar 

  • Kakuta Y, Horio T, Takahashi Y and Fukuyama K (2001) Crystal structure of Echerichia coli Fdx, an adrenodoxin-type ferredoxin involved in the assembly of iron-sulfur clusters. Biochemistry 37: 11007–11012

    Article  CAS  Google Scholar 

  • Karlsson A, Beharry ZM, Eby DM, Coulter ED, Neidle EL, Kurtz Jr DM, Ekulund H and Ramaswamy S (2002) X-ray crystal structure of benzoate 1,2-dioxygenase reductase from Acinetobacter sp. strain ADPl. J Mol Biol 318: 261–272

    Article  PubMed  CAS  Google Scholar 

  • Karplus PA and Bruns CM (1994) Structure-function relations for ferredoxin reductase. J Bioenerg Biomemb 26: 89–99

    Article  CAS  Google Scholar 

  • Karplus PA, Daniels MJ and Harriott JR (1991) Atomic structure of ferredoxin-NADPH+ reductase: prototype for a structurally novel flavoenzyme family. Science 251: 60–66 299

    PubMed  CAS  Google Scholar 

  • Kimata Y and Hase T (1989) Localization of ferredoxin isoproteins in mesophyll and bundle sheath cells in maize leaf. Plant Physiol 89: 1193–1197

    PubMed  CAS  Google Scholar 

  • Knaff DB and Hirasawa M (1991) Ferredoxin-dependent chloroplast enzymes. Biochim Biophys Acta 1056: 93–125

    PubMed  CAS  Google Scholar 

  • Kraulis P (1991) Similarity of protein G and ubiquitin. Science 254: 581–582

    PubMed  CAS  Google Scholar 

  • Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24: 946–950

    Article  Google Scholar 

  • Kurisu G, Kusunoki M, Katoh E, Yamazaki T, Teshima K, Onda Y, Kimata-Ariga Y and Hase T (2001) Structure of the electron transfer complex between ferredoxin and ferredoxin-NADP+ reductase. Nat Struct Biol 8: 117–121

    Article  PubMed  CAS  Google Scholar 

  • Lelong C, Sétif P, Bottin H, André F and Neumann JM (1995) 1H and 15N NMR sequential assignment, secondary structure, and tertiary fold of [2Fe-2S] ferredoxin from Synechocystis sp. PCC 6803. Biochemistry 34: 14462–14473

    Article  PubMed  CAS  Google Scholar 

  • Lovenberg W (ed) (1973, 1977) Iron Sulfur Proteins, Vol I-III. Academic Press, New York

    Google Scholar 

  • Mason JI and Boyd GS (1971) The chloreterol side chain cleavage enzyme system in mitochondria of human term placenta. Eur J Biochem 21: 308–321

    Article  PubMed  CAS  Google Scholar 

  • Matsubara H and Saeki K (1992) Structural and functional diversity of ferredoxins and related proteins. Adv Inorg Chem 38: 223–280

    CAS  Google Scholar 

  • Matsubara H and Sasaki RM (1968) Spinach ferredoxin II: Triptic, chymotryptic, and thermolytic peptides, and complete amino acid sequence. J Biol Chem 243: 1732–1757

    PubMed  CAS  Google Scholar 

  • Matsumura T, Sakakibara H, Nakano R, Kimata Y, Sugiyama T and Hase T (1997) A nitrate-inducible ferredoxin in maize roots: genomic organization and differential expression of two nonphotosynthetic ferredoxin isoproteins. Plant Physiol 114: 653–660

    Article  PubMed  CAS  Google Scholar 

  • Mayerle JJ, Frankel RB, Holms RH, Ibers JA, Phillips WD and Weiher JF (1973) Synthetic analogs of the active sites of ironsulfur proteins: structure and properties of bis[o-xyly1dithiolate-µ2-sulfidoferrate(III)], an analog of the 2Fe-2S proteins. Proc Natl Acad Sci USA 70: 2429–2433

    Article  PubMed  CAS  Google Scholar 

  • McRee DE (1999) XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density. J Struct Biol 125: 156–165

    Article  PubMed  CAS  Google Scholar 

  • Merritt EA and Bacon DJ (1997) Raster3D photorealistic molecular graphics. Meth Enzymol 277: 505–524

    Article  CAS  PubMed  Google Scholar 

  • Messerschmidt A, Huber R, Poulos T and Wieghardt K (ed) (2001) Handbook of Metalloproteins, Vol I. John Wiley & Sons, UK

    Google Scholar 

  • Morales R, Charon M-H, Hudry-Clergeon G, Pètillot Y, Norager S, Medina M and Frey M (1999) Refined X-ray structures of the oxidized, at 1.3 Å, and reduced, at 1.17 Å, [2Fe-2S] ferredoxin from the cyanobacterium Anabaena PCC7119 show redox-linked conformational changes. Biochemistry 38: 15764–15773

    Article  PubMed  CAS  Google Scholar 

  • Morales R, Charon M-H, Kachalova G, Serre L, Medina M, Gomez-Moreno C and Frey M (2000) A redox-dependent interaction between two electron-transfer partners involved in photosynthesis. EMBO Rep 1: 271–276

    Article  PubMed  CAS  Google Scholar 

  • Mortenson LE, Valentine RC and Carnahan JE (1962) An electron transport factor from Clostridium pasteurianum. Biochem Biophys Res Commun 7: 448–452

    Article  PubMed  CAS  Google Scholar 

  • Mossessova E and Lima CD (2000) Ulpl-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol Cell 5: 865–876

    Article  PubMed  CAS  Google Scholar 

  • Müller A, Müller JJ, Muller YA, Uhlmann H, Bernhardt R and Heinemann U (1998) New aspect of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, Adx(4-108). Structure 6: 269–280

    Article  PubMed  Google Scholar 

  • Nakamura M, Saeki K and Takahashi Y (1999) Hyperproduction of recombinant ferredoxins in Escherichia coll by coexpression of the ORF1-ORF2-iscS-iscU-iscA-hscB-hscAfdx-ORF3 gene cluster. J Biochem 126: 10–18

    PubMed  CAS  Google Scholar 

  • Nassar N, Horn Gudrum, Herrmann C, Scherer A, McCormick F and Wittinghofer A (1995) The 2.2 Åcrystal structure of the Ras-binding domain of the serine/threonine kinase c-Rafl1 in complex with Rap lA and a GTP analogue. Nature 375: 554–560

    Article  PubMed  CAS  Google Scholar 

  • Nishiyama D (2003) Structural studies of Fd II from Equisetum arvense at 1.2 Åresolution. Thesis, Osaka University

  • Onda Y, Matsumura T, Kimata-Ariga Y, Sakakibara H, Sugiyama T and Hase T (2000) Differential interaction of maize root ferredoxin: NADP+ oxidoreducatse with photosynthetic and non-photosynthetic ferredoxin isoproteins. Plant Physiol 123: 1037–1045

    Article  PubMed  CAS  Google Scholar 

  • Orengo C (1994) Classification of protein folds. Curr Opin Struct Biol 4: 429–440

    Article  CAS  Google Scholar 

  • Otomo T, Sakahira H, Uegaki K, Nagata S and Yamazaki T (2000) Structure of the heterodimeric complex between CAD domains of CAD and ICAD. Nat Struct Biol 7: 658–662

    Article  PubMed  CAS  Google Scholar 

  • Overington JP (1992) Comparison of three-dimensional structures of homologous proteins. Curr Opin Struct Biol 2: 394–401

    Article  CAS  Google Scholar 

  • Ozaki Y, Kyogoku Y, Hase T, Matsubara H, Oshima T, Ueyama N, Nakamura Y and Iriyama K (1986) Resonance Raman characterization of iron-sulfur cores in various ferredoxins and their model compounds. In: Matsubara H, Katsube Y and Wada K (eds) Iron-Sulfur Protein Research. Japan Scientific Societies Press, Tokyo

    Google Scholar 

  • Peterson JA and Graham-Lorence SE (1995) Cytochrome P450: Structure, Mechanism and Biochemistry, 2nd ed, pp 151–180. Plenum Press, New York

    Google Scholar 

  • Pochapsky TC, Janin NU, Kuti M, Lyons TA and Heymont J (1999) Refined model for the solution structure of oxidized putidaredoxin. Biochemistry 38: 4681–4690

    Article  PubMed  CAS  Google Scholar 

  • Rebelo J, Macieira S, Dias JM, Huber R, Ascenso CS, Rusnak F, Moura JJG, Moura I and Romco MJ (2000) Gene sequence and crystal structure of the aldehyde oxidoreductase from Desulfovibrio desulfuricans ATCC 27774. J Mol Biol 297: 135–146

    Article  PubMed  CAS  Google Scholar 

  • Rypniewski WR, Breiter DR, Benning MM, Wesenberg G, Oh BH, Markley JL, Rayment I and Holden HM (1991) Crystallization and structure determination to 2.5 Åresolution of the oxidized [2Fe-2S] ferredoxin isolated from Anabaena 7120. Biochemistry 30: 4126–4131

    Article  PubMed  CAS  Google Scholar 

  • Sticht H and Rösch P (1998) The structure of iron-sulfur proteins. Biophys Mol Biol 70: 95–136

    Article  CAS  Google Scholar 

  • Suzuki A, Oaks A, Jacquot J-P, Vidal J and Gadal P (1985) An electron tranport system in maize roots for reactions of glutamate synthase and nitrite reductase: physiological and 300 immunochemical properties of the electron carrier and pyridine nucleotide reductase. Plant Physiol 78: 374–378

    Article  PubMed  CAS  Google Scholar 

  • Tagawa K and Arnon DI (1962) Ferredoxins as electron carriers in photosynthesis and in the biological production and consumption of hydrogen gas. Nature 195: 537–543

    Article  PubMed  CAS  Google Scholar 

  • Takahashi Y and Nakamura M (1999) Functional assignment of the ORF2-iscS-iscU-iscA-hscB-hscA-fdx-ORF3 gene cluster involved in the assembly of Fe-S clusters in Escherichia coli. J Biochem 126: 917–926

    PubMed  CAS  Google Scholar 

  • Teshima K, Fujita S, Hirose S, Nishiyama D, Kurisu G, Kusunoki M, Kimata-Ariga Y and Hase T (2003) A ferredoxin Arg-Glu pair important for efficient electron transfer between ferredoxin and ferredoxin-NADP+ reductase. FEBS Lett 546: 189–194

    Article  PubMed  CAS  Google Scholar 

  • Tokumoto U and Takahashi Y (2001) Genetic analysis of the isc operon in Escherichia coli involved in the biogenesis of cellular iron-sulfur proteins. J Biochem 130: 63–71

    PubMed  CAS  Google Scholar 

  • Tsukihara T, Fukuyama K, Nakamura M, Katsube Y, Tanaka N, Kakudo M, Wada K, Hase T and Matsubara H (1981) XRay analysis of a [2Fe-2S] ferredoxin from Spirulina platensis: Main chain fold and location of side chains at 2.5 Å resolution. J Biochem 90: 1763–1773

    CAS  Google Scholar 

  • Tsukihara T, Fukuyama K, Mizushima M, Harioka T, Kusunoki M, Katsube Y, Hase T and Matsubara H (1990) Structure of the [2Fe-2S] ferredoxin I from the blue-green alga Aphanothece sacrum at 2.2 Åresolution. J Mol Biol 216: 399–410

    PubMed  CAS  Google Scholar 

  • Vriend G and Sander C (1991) Detection of common threedimensional substructures in proteins. Proteins Struct Funct Genet 11: 52–58

    Article  PubMed  CAS  Google Scholar 

  • Wada K, Matsubara H, Chain RK and Arnon DI (1981) A comparative study of the biological activities of two molecular species of chloroplast-type ferredoxins. Plant Cell Physiol 22: 275–281

    CAS  Google Scholar 

  • Wada K, Onda M and Matsubara H (1986) Ferredoxin isolated from plant non-photosynthetic tissues: purification and characterization. Plant Cell Physiol 27: 407–415

    CAS  Google Scholar 

  • Wakabayashi S, Hase T, Wada K, Matsubara H, Suzuki K and Takaichi S (1978) Amino acid sequences of two ferredoxins from pokeweed Phytolacca americana. J Biochem 83: 1305–1319

    PubMed  CAS  Google Scholar 

  • Yankovskaya V, Horsefield R, Törnroth S, Luna-Chavez C, Miyoshi H, Léger C, Byrne B, Cecchini G and Iwata S (2003) Architecture of succinate dehydrogenase and reactive oxygen species generation. Science 299: 700–704

    Article  PubMed  CAS  Google Scholar 

  • Zanetti G, Binda C and Aliverti A (2001) The [2Fe-2S] ferredoxins. In: Messerschmidt A, Huber R, Poulos T and Wieghardt K (eds) Handbook of Metalloproteins, pp 532–542. John Wiley & Sons, UK

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Keiichi Fukuyama.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fukuyama, K. Structure and Function of Plant-Type Ferredoxins. Photosynthesis Research 81, 289–301 (2004). https://doi.org/10.1023/B:PRES.0000036882.19322.0a

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/B:PRES.0000036882.19322.0a

Navigation