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PDBsum entry 1fnc
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Oxidoreductase (NADP+(a),ferredoxin(a)) PDB id
1fnc

 

 

 

 

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Contents
Protein chain
296 a.a. *
Ligands
SO4
FDA
A2P
Waters ×216
* Residue conservation analysis
PDB id:
1fnc
Name: Oxidoreductase (NADP+(a),ferredoxin(a))
Title: Refined crystal structure of spinach ferredoxin reductase at 1.7 angstroms resolution: oxidized, reduced, and 2'-phospho-5'-amp bound states
Structure: Ferredoxin-NADP+ reductase. Chain: a. Engineered: yes
Source: Spinacia oleracea. Spinach. Organism_taxid: 3562
Resolution:
2.00Å     R-factor:   0.149    
Authors: C.M.Bruns,P.A.Karplus
Key ref: C.M.Bruns and P.A.Karplus (1995). Refined crystal structure of spinach ferredoxin reductase at 1.7 A resolution: oxidized, reduced and 2'-phospho-5'-AMP bound states. J Mol Biol, 247, 125-145. PubMed id: 7897656
Date:
05-Jan-95     Release date:   20-Apr-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P00455  (FENR_SPIOL) -  Ferredoxin--NADP reductase, chloroplastic from Spinacia oleracea
Seq:
Struc: 		369 a.a.
296 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.18.1.2  - ferredoxin--NADP(+) reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Methionine Synthase
      Reaction: 2 reduced [2Fe-2S]-[ferredoxin] + NADP+ + H+ = 2 oxidized [2Fe-2S]- [ferredoxin] + NADPH
2 × reduced [2Fe-2S]-[ferredoxin]
 + NADP(+)
 + H(+)
 = 2 × oxidized [2Fe-2S]- [ferredoxin]
 + NADPH
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FDA) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
J Mol Biol 247:125-145 (1995)
PubMed id: 7897656  
 
 
Refined crystal structure of spinach ferredoxin reductase at 1.7 A resolution: oxidized, reduced and 2'-phospho-5'-AMP bound states.
C.M.Bruns, P.A.Karplus.
 
  ABSTRACT  
 
The crystal structure of spinach ferredoxin-NADP(+)-oxidoreductase (FNR), determined by multiple isomorphous replacement at 2.6 A resolution, has been refined at 1.7 A resolution to an R-factor of 17.9%. The structure of FNR bound to the competitive inhibitor 2'-phospho-5'-AMP (P-AMP) has also been refined at 1.7 A to an R-factor of 17.4% and dithionite-reduced/P-AMP-bound FNR has been refined at 2.0 A to an R-factor of 14.9%. The P-AMP-bound structure was used to construct a model for the binding of NADP+. Over 200 solvation sites were included in each structure, and many of the best defined solvation sites stabilize buried turns. A bulk solvent correction obviated the need for a low-resolution data cutoff. An acidic side-chain likely to be responsible for the low pH requirement for crystallization has been identified. Three large networks of the hydrophobic side-chains help define the FNR structure. One of these contains a large cavity far from the active site, which coincides with the lone site of sequence heterogeneity in FNR, and may provide a site for membrane attachment. The reduced structure shows that Ser96 moves toward atom N-5 of FAD and a water molecule moves toward atom N-1 of FAD, while the flavin moiety remains planar. Possible sources of a proton that must be picked up upon reduction are discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20974920 F.Alte, A.Stengel, J.P.Benz, E.Petersen, J.Soll, M.Groll, and B.Bölter (2010).
Ferredoxin:NADPH oxidoreductase is recruited to thylakoids by binding to a polyproline type II helix in a pH-dependent manner.
  Proc Natl Acad Sci U S A, 107, 19260-19265.
PDB code: 3mhp
19759024 A.Korn, G.Ajlani, B.Lagoutte, A.Gall, and P.Sétif (2009).
Ferredoxin:NADP+ oxidoreductase association with phycocyanin modulates its properties.
  J Biol Chem, 284, 31789-31797.  
19523113 E.Balconi, A.Pennati, D.Crobu, V.Pandini, R.Cerutti, G.Zanetti, and A.Aliverti (2009).
The ferredoxin-NADP+ reductase/ferredoxin electron transfer system of Plasmodium falciparum.
  FEBS J, 276, 3825-3836.  
19583765 M.Medina (2009).
Structural and mechanistic aspects of flavoproteins: photosynthetic electron transfer from photosystem I to NADP+.
  FEBS J, 276, 3942-3958.  
19708087 N.Shibata, Y.Ueda, D.Takeuchi, Y.Haruyama, S.Kojima, J.Sato, Y.Niimura, M.Kitamura, and Y.Higuchi (2009).
Structure analysis of the flavoredoxin from Desulfovibrio vulgaris Miyazaki F reveals key residues that discriminate the functions and properties of the flavin reductase family.
  FEBS J, 276, 4840-4853.  
19243237 T.Senda, M.Senda, S.Kimura, and T.Ishida (2009).
Redox control of protein conformation in flavoproteins.
  Antioxid Redox Signal, 11, 1741-1766.  
18605699 A.Wang, J.C.Rodríguez, H.Han, E.Schönbrunn, and M.Rivera (2008).
X-ray crystallographic and solution state nuclear magnetic resonance spectroscopic investigations of NADP+ binding to ferredoxin NADP reductase from Pseudomonas aeruginosa.
  Biochemistry, 47, 8080-8093.
PDB code: 3crz
18253859 J.Grzyb, P.Malec, I.Rumak, M.Garstka, and K.Strzałka (2008).
Two isoforms of ferredoxin:NADP(+) oxidoreductase from wheat leaves: purification and initial biochemical characterization.
  Photosynth Res, 96, 99.  
18279389 M.A.Musumeci, A.K.Arakaki, D.V.Rial, D.L.Catalano-Dupuy, and E.A.Ceccarelli (2008).
Modulation of the enzymatic efficiency of ferredoxin-NADP(H) reductase by the amino acid volume around the catalytic site.
  FEBS J, 275, 1350-1366.  
18156264 S.Nijvipakul, J.Wongratana, C.Suadee, B.Entsch, D.P.Ballou, and P.Chaiyen (2008).
LuxG is a functioning flavin reductase for bacterial luminescence.
  J Bacteriol, 190, 1531-1538.  
17945509 S.S.Negi, A.A.Carol, S.Pandya, W.Braun, and L.E.Anderson (2008).
Co-localization of glyceraldehyde-3-phosphate dehydrogenase with ferredoxin-NADP reductase in pea leaf chloroplasts.
  J Struct Biol, 161, 18-30.  
17958910 A.S.Nascimento, D.L.Catalano-Dupuy, A.Bernardes, M.d.e. .O.Neto, M.A.Santos, E.A.Ceccarelli, and I.Polikarpov (2007).
Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+.
  BMC Struct Biol, 7, 69.
PDB codes: 2rc5 2rc6
17277060 H.Iwaki, T.Muraki, S.Ishihara, Y.Hasegawa, K.N.Rankin, T.Sulea, J.Boyd, and P.C.Lau (2007).
Characterization of a pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis.
  J Bacteriol, 189, 3502-3514.  
17192259 Y.H.Lee, K.Tamura, M.Maeda, M.Hoshino, K.Sakurai, S.Takahashi, T.Ikegami, T.Hase, and Y.Goto (2007).
Cores and pH-dependent dynamics of ferredoxin-NADP+ reductase revealed by hydrogen/deuterium exchange.
  J Biol Chem, 282, 5959-5967.  
16027125 H.Tsuge, R.Kawakami, H.Sakuraba, H.Ago, M.Miyano, K.Aki, N.Katunuma, and T.Ohshima (2005).
Crystal structure of a novel FAD-, FMN-, and ATP-containing L-proline dehydrogenase complex from Pyrococcus horikoshii.
  J Biol Chem, 280, 31045-31049.
PDB code: 1y56
15560800 D.L.Dupuy, D.V.Rial, and E.A.Ceccarelli (2004).
Inhibition of pea ferredoxin-NADP(H) reductase by Zn-ferrocyanide.
  Eur J Biochem, 271, 4582-4593.  
15386621 M.Prudêncio, and M.Ubbink (2004).
Transient complexes of redox proteins: structural and dynamic details from NMR studies.
  J Mol Recognit, 17, 524-539.  
15502298 S.Bando, T.Takano, T.Yubisui, K.Shirabe, M.Takeshita, and A.Nakagawa (2004).
Structure of human erythrocyte NADH-cytochrome b5 reductase.
  Acta Crystallogr D Biol Crystallogr, 60, 1929-1934.
PDB code: 1umk
12887584 J.F.Palatnik, V.B.Tognetti, H.O.Poli, R.E.Rodríguez, N.Blanco, M.Gattuso, M.R.Hajirezaei, U.Sonnewald, E.M.Valle, and N.Carrillo (2003).
Transgenic tobacco plants expressing antisense ferredoxin-NADP(H) reductase transcripts display increased susceptibility to photo-oxidative damage.
  Plant J, 35, 332-341.  
14500716 J.Tejero, M.Martínez-Julvez, T.Mayoral, A.Luquita, J.Sanz-Aparicio, J.A.Hermoso, J.K.Hurley, G.Tollin, C.Gómez-Moreno, and M.Medina (2003).
Involvement of the pyrophosphate and the 2'-phosphate binding regions of ferredoxin-NADP+ reductase in coenzyme specificity.
  J Biol Chem, 278, 49203-49214.
PDB codes: 1h42 1ogi 1ogj
12417584 L.Filisetti, M.Fontecave, and V.Niviere (2003).
Mechanism and substrate specificity of the flavin reductase ActVB from Streptomyces coelicolor.
  J Biol Chem, 278, 296-303.  
12709048 N.Carrillo, and E.A.Ceccarelli (2003).
Open questions in ferredoxin-NADP+ reductase catalytic mechanism.
  Eur J Biochem, 270, 1900-1915.  
12423341 D.V.Rial, V.A.Lombardo, E.A.Ceccarelli, and J.Ottado (2002).
The import of ferredoxin-NADP+ reductase precursor into chloroplasts is modulated by the region between the transit peptide and the mature core of the protein.
  Eur J Biochem, 269, 5431-5439.  
12047373 M.Faro, C.Gómez-Moreno, M.Stankovich, and M.Medina (2002).
Role of critical charged residues in reduction potential modulation of ferredoxin-NADP+ reductase.
  Eur J Biochem, 269, 2656-2661.  
12383252 M.Faro, S.Frago, T.Mayoral, J.A.Hermoso, J.Sanz-Aparicio, C.Gómez-Moreno, and M.Medina (2002).
Probing the role of glutamic acid 139 of Anabaena ferredoxin-NADP+ reductase in the interaction with substrates.
  Eur J Biochem, 269, 4938-4947.
PDB code: 1gr1
12426385 M.Küchler, S.Decker, F.Hörmann, J.Soll, and L.Heins (2002).
Protein import into chloroplasts involves redox-regulated proteins.
  EMBO J, 21, 6136-6145.  
11844106 M.R.Hajirezaei, M.Peisker, H.Tschiersch, J.F.Palatnik, E.M.Valle, N.Carrillo, and U.Sonnewald (2002).
Small changes in the activity of chloroplastic NADP(+)-dependent ferredoxin oxidoreductase lead to impaired plant growth and restrict photosynthetic activity of transgenic tobacco plants.
  Plant J, 29, 281-293.  
11329262 A.W.Munro, M.A.Noble, L.Robledo, S.N.Daff, and S.K.Chapman (2001).
Determination of the redox properties of human NADPH-cytochrome P450 reductase.
  Biochemistry, 40, 1956-1963.  
11525168 H.J.Chiu, E.Johnson, I.Schröder, and D.C.Rees (2001).
Crystal structures of a novel ferric reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus and its complex with NADP+.
  Structure, 9, 311-319.
PDB codes: 1i0r 1i0s
11369223 M.R.Jones, and P.K.Fyfe (2001).
Photosynthesis: new light on biological oxygen production.
  Curr Biol, 11, R318-R321.  
11761334 S.C.Tu (2001).
Reduced flavin: donor and acceptor enzymes and mechanisms of channeling.
  Antioxid Redox Signal, 3, 881-897.  
11123926 A.Gutierrez, O.Doehr, M.Paine, C.R.Wolf, N.S.Scrutton, and G.C.Roberts (2000).
Trp-676 facilitates nicotinamide coenzyme exchange in the reductive half-reaction of human cytochrome P450 reductase: properties of the soluble W676H and W676A mutant reductases.
  Biochemistry, 39, 15990-15999.  
10913298 C.M.Reynolds, and L.B.Poole (2000).
Attachment of the N-terminal domain of Salmonella typhimurium AhpF to Escherichia coli thioredoxin reductase confers AhpC reductase activity but does not affect thioredoxin reductase activity.
  Biochemistry, 39, 8859-8869.  
11087941 I.Curdt, B.B.Singh, M.Jakoby, W.Hachtel, and H.Böhme (2000).
Identification of amino acid residues of nitrite reductase from Anabaena sp. PCC 7120 involved in ferredoxin binding.
  Biochim Biophys Acta, 1543, 60-68.  
10819972 M.B.Murataliev, and R.Feyereisen (2000).
Interaction of NADP(H) with oxidized and reduced P450 reductase during catalysis. Studies with nucleotide analogues.
  Biochemistry, 39, 5066-5074.  
11256611 R.Morales, M.H.Charon, G.Kachalova, L.Serre, M.Medina, C.Gómez-Moreno, and M.Frey (2000).
A redox-dependent interaction between two electron-transfer partners involved in photosynthesis.
  EMBO Rep, 1, 271-276.  
10651039 T.Mayoral, M.Medina, J.Sanz-Aparicio, C.Gómez-Moreno, and J.A.Hermoso (2000).
Structural basis of the catalytic role of Glu301 in Anabaena PCC 7119 ferredoxin-NADP+ reductase revealed by x-ray crystallography.
  Proteins, 38, 60-69.
PDB code: 1b2r
10026149 A.L.Shen, D.S.Sem, and C.B.Kasper (1999).
Mechanistic studies on the reductive half-reaction of NADPH-cytochrome P450 oxidoreductase.
  J Biol Chem, 274, 5391-5398.  
10353815 M.Ingelman, S.Ramaswamy, V.Nivière, M.Fontecave, and H.Eklund (1999).
Crystal structure of NAD(P)H:flavin oxidoreductase from Escherichia coli.
  Biochemistry, 38, 7040-7049.
PDB code: 1qfj
10373427 V.Nivière, F.Fieschi, J.L.Dećout, and M.Fontecave (1999).
The NAD(P)H:flavin oxidoreductase from Escherichia coli. Evidence for a new mode of binding for reduced pyridine nucleotides.
  J Biol Chem, 274, 18252-18260.  
15012211 W.H.Campbell (1999).
NITRATE REDUCTASE STRUCTURE, FUNCTION AND REGULATION: Bridging the Gap between Biochemistry and Physiology.
  Annu Rev Plant Physiol Plant Mol Biol, 50, 277-303.  
9915836 Y.S.Jung, V.A.Roberts, C.D.Stout, and B.K.Burgess (1999).
Complex formation between Azotobacter vinelandii ferredoxin I and its physiological electron donor NADPH-ferredoxin reductase.
  J Biol Chem, 274, 2978-2987.  
9852055 A.Aliverti, Z.Deng, D.Ravasi, L.Piubelli, P.A.Karplus, and G.Zanetti (1998).
Probing the function of the invariant glutamyl residue 312 in spinach ferredoxin-NADP+ reductase.
  J Biol Chem, 273, 34008-34015.
PDB codes: 1bx0 1bx1 1frq
10089511 C.Binda, A.Coda, A.Aliverti, G.Zanetti, and A.Mattevi (1998).
Structure of the mutant E92K of [2Fe-2S] ferredoxin I from Spinacia oleracea at 1.7 A resolution.
  Acta Crystallogr D Biol Crystallogr, 54, 1353-1358.
PDB code: 1a70
9893942 C.Gómez-Moreno, M.Martínez-Júlvez, M.Medina, J.K.Hurley, and G.Tollin (1998).
Protein-protein interaction in electron transfer reactions: the ferredoxin/flavodoxin/ferredoxin:NADP+ reductase system from Anabaena.
  Biochimie, 80, 837-846.  
  9865948 G.Sridhar Prasad, N.Kresge, A.B.Muhlberg, A.Shaw, Y.S.Jung, B.K.Burgess, and C.D.Stout (1998).
The crystal structure of NADPH:ferredoxin reductase from Azotobacter vinelandii.
  Protein Sci, 7, 2541-2549.
PDB code: 1a8p
9922134 M.Martínez-Júlvez, J.Hermoso, J.K.Hurley, T.Mayoral, J.Sanz-Aparicio, G.Tollin, C.Gómez-Moreno, and M.Medina (1998).
Role of Arg100 and Arg264 from Anabaena PCC 7119 ferredoxin-NADP+ reductase for optimal NADP+ binding and electron transfer.
  Biochemistry, 37, 17680-17691.
PDB code: 1bjk
9753447 M.Martínez-Júlvez, M.Medina, J.K.Hurley, R.Hafezi, T.B.Brodie, G.Tollin, and C.Gómez-Moreno (1998).
Lys75 of Anabaena ferredoxin-NADP+ reductase is a critical residue for binding ferredoxin and flavodoxin during electron transfer.
  Biochemistry, 37, 13604-13613.  
9485422 M.Medina, M.Martinez-Júlvez, J.K.Hurley, G.Tollin, and C.Gómez-Moreno (1998).
Involvement of glutamic acid 301 in the catalytic mechanism of ferredoxin-NADP+ reductase from Anabaena PCC 7119.
  Biochemistry, 37, 2715-2728.  
9511808 S.Schmitz, M.Martínez-Júlvez, C.Gómez-Moreno, and H.Böhme (1998).
Interaction of positively charged amino acid residues of recombinant, cyanobacterial ferredoxin:NADP+ reductase with ferredoxin probed by site directed mutagenesis.
  Biochim Biophys Acta, 1363, 85-93.  
9724550 T.J.Kirksey, S.W.Kwan, and C.W.Abell (1998).
Arginine-42 and threonine-45 are required for FAD incorporation and catalytic activity in human monoamine oxidase B.
  Biochemistry, 37, 12360-12366.  
9718311 V.Nivière, M.A.Vanoni, G.Zanetti, and M.Fontecave (1998).
Reaction of the NAD(P)H:flavin oxidoreductase from Escherichia coli with NADPH and riboflavin: identification of intermediates.
  Biochemistry, 37, 11879-11887.  
9115439 C.Tarricone, A.Galizzi, A.Coda, P.Ascenzi, and M.Bolognesi (1997).
Unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from Vitreoscilla sp.
  Structure, 5, 497-507.
PDB codes: 1vhb 2vhb
9095194 K.Diederichs, and P.A.Karplus (1997).
Improved R-factors for diffraction data analysis in macromolecular crystallography.
  Nat Struct Biol, 4, 269-275.  
9237990 M.Wang, D.L.Roberts, R.Paschke, T.M.Shea, B.S.Masters, and J.J.Kim (1997).
Three-dimensional structure of NADPH-cytochrome P450 reductase: prototype for FMN- and FAD-containing enzymes.
  Proc Natl Acad Sci U S A, 94, 8411-8416.
PDB code: 1amo
8755724 A.L.Shen, and C.B.Kasper (1996).
Role of Ser457 of NADPH-cytochrome P450 oxidoreductase in catalysis and control of FAD oxidation-reduction potential.
  Biochemistry, 35, 9451-9459.  
8880927 H.Nishida, and K.Miki (1996).
Electrostatic properties deduced from refined structures of NADH-cytochrome b5 reductase and the other flavin-dependent reductases: pyridine nucleotide-binding and interaction with an electron-transfer partner.
  Proteins, 26, 32-41.  
8774710 M.E.Corrado, A.Aliverti, G.Zanetti, and S.G.Mayhew (1996).
Analysis of the oxidation-reduction potentials of recombinant ferredoxin-NADP+ reductase from spinach chloroplasts.
  Eur J Biochem, 239, 662-667.  
8663185 V.Nivière, F.Fieschi, J.L.Décout, and M.Fontecave (1996).
Is the NAD(P)H:flavin oxidoreductase from Escherichia coli a member of the ferredoxin-NADP+ reductase family?. Evidence for the catalytic role of serine 49 residue.
  J Biol Chem, 271, 16656-16661.  
  8557026 U.Ermler, R.A.Siddiqui, R.Cramm, and B.Friedrich (1995).
Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution.
  EMBO J, 14, 6067-6077.
PDB code: 1cqx
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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