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PDBsum entry 1que

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Oxidoreductase PDB id
1que
Jmol
Contents
Protein chain
303 a.a. *
Ligands
SO4
FAD
Waters ×325
* Residue conservation analysis
PDB id:
1que
Name: Oxidoreductase
Title: X-ray structure of the ferredoxin:nadp+ reductase from the cyanobacterium anabaena pcc 7119 at 1.8 angstroms
Structure: Ferredoxin--NADP+ reductase. Chain: a. Synonym: fnr. Ec: 1.18.1.2
Source: Nostoc sp.. Organism_taxid: 1168. Strain: pcc 7119
Resolution:
1.80Å     R-factor:   0.172     R-free:   0.214
Authors: L.Serre,M.Frey,F.M.D.Vellieux
Key ref:
L.Serre et al. (1996). X-ray structure of the ferredoxin:NADP+ reductase from the cyanobacterium Anabaena PCC 7119 at 1.8 A resolution, and crystallographic studies of NADP+ binding at 2.25 A resolution. J Mol Biol, 263, 20-39. PubMed id: 8890910 DOI: 10.1006/jmbi.1996.0553
Date:
06-Jul-96     Release date:   15-May-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21890  (FENR_ANASO) -  Ferredoxin--NADP reductase
Seq:
Struc:
440 a.a.
303 a.a.*
Key:    PfamA domain  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 ferredoxin + NADP+ + H+ = 2 oxidized ferredoxin + NADPH
2 × reduced ferredoxin
+ NADP(+)
+ H(+)
= 2 × oxidized ferredoxin
+ NADPH
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1996.0553 J Mol Biol 263:20-39 (1996)
PubMed id: 8890910  
 
 
X-ray structure of the ferredoxin:NADP+ reductase from the cyanobacterium Anabaena PCC 7119 at 1.8 A resolution, and crystallographic studies of NADP+ binding at 2.25 A resolution.
L.Serre, F.M.Vellieux, M.Medina, C.Gomez-Moreno, J.C.Fontecilla-Camps, M.Frey.
 
  ABSTRACT  
 
The crystal structure of the ferredoxin:NADP+ reductase (FNR) from the cyanobacterium Anabaena PCC 7119 has been determined at 2.6 A resolution by multiple isomorphous replacement and refined using 15.0 A to 1.8 A data, collected at 4 degrees C, to an R-factor of 0.172. The model includes 303 residues, the flavin adenine dinucleotide cofactor (FAD), one sulfate ion located at the putative NADP+ binding site and 328 water molecule sites. The structure of Anabaena FNR, including FAD, a network of intrinsic water molecules and a large hydrophobic cavity in the C-terminal domain, resembles that of the spinach enzyme. The major differences concern the additional short alpha-helix (residues 172 to 177 in Anabaena FNR) and residues Arg 100 and Arg 233 which binds NADP+ instead of Lys 116 and Lys 244 in the spinach enzyme. Crystals of a complex of Anabaena FNR with NADP+ were obtained. The model of the complex has been refined using 15 A to 2.25 A X-ray data, collected at -170 degrees C, to an R-factor of 0.186. This model includes 295 residues, FAD, the full NADP+ (with an occupancy of 0.8) and 444 water molecules. The 2'-5' adenine moiety of NADP+ binds to the protein as 2'-phospho-5'-AMP to the spinach FNR. The nicotinamide moiety is turned towards the surface of the protein instead of stacking onto the FAD isoalloxazine ring as would be required for hydride transfer. The model of the complex agrees with previous biochemical studies as residues Arg 100 and Arg 233 are involved in NADP+ binding and residues Arg77, Lys 53 and Lys 294, located on the FAD side of the enzyme, remain free to interact with ferredoxin and flavodoxin, the physiological partners of ferredoxin: NADP reductase.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Interaction between FNR and ferredoxin. The charged residues, which are probably involved in the binding of FNR with ferredoxin and are currently mutated, are represented by thick lines.
Figure 8.
Figure 8. A stereoscopic view of the difference electron density at the NADP + site (contoured at 2s) calculated with phases from a model obtained by refining the native FNR X-ray model at 1.8 Å resolution (omitting residue 1 to 8, the sulfate ion and the water molecules) by simulated annealing and energy minimization against the amplitudes from the FNR-NADP + crystal. The final NADP + position is represented.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 263, 20-39) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20878669 H.Komori, D.Seo, T.Sakurai, and Y.Higuchi (2010).
Crystal structure analysis of Bacillus subtilis ferredoxin-NADP(+) oxidoreductase and the structural basis for its substrate selectivity.
  Protein Sci, 19, 2279-2290.
PDB codes: 3lzw 3lzx
20124342 L.Lim, and G.I.McFadden (2010).
The evolution, metabolism and functions of the apicoplast.
  Philos Trans R Soc Lond B Biol Sci, 365, 749-763.  
19583765 M.Medina (2009).
Structural and mechanistic aspects of flavoproteins: photosynthetic electron transfer from photosystem I to NADP+.
  FEBS J, 276, 3942-3958.  
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
17828614 F.M.Morsy, M.Nakajima, T.Yoshida, T.Fujiwara, T.Sakamoto, and K.Wada (2008).
Subcellular localization of ferredoxin-NADP(+) oxidoreductase in phycobilisome retaining oxygenic photosysnthetic organisms.
  Photosynth Res, 95, 73-85.  
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.  
18260112 M.Medina, R.Abagyan, C.Gómez-Moreno, and J.Fernandez-Recio (2008).
Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin.
  Proteins, 72, 848-862.  
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
17335513 M.Lintala, Y.Allahverdiyeva, H.Kidron, M.Piippo, N.Battchikova, M.Suorsa, E.Rintamäki, T.A.Salminen, E.M.Aro, and P.Mulo (2007).
Structural and functional characterization of ferredoxin-NADP+-oxidoreductase using knock-out mutants of Arabidopsis.
  Plant J, 49, 1041-1052.  
  16820688 A.S.Nascimento, T.Ferrarezi, D.L.Catalano-Dupuy, E.A.Ceccarelli, and I.Polikarpov (2006).
Crystallization and preliminary X-ray diffraction studies of ferredoxin reductase from Leptospira interrogans.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 662-664.  
15894798 N.Cassan, B.Lagoutte, and P.Sétif (2005).
Ferredoxin-NADP+ reductase. Kinetics of electron transfer, transient intermediates, and catalytic activities studied by flash-absorption spectroscopy with isolated photosystem I and ferredoxin.
  J Biol Chem, 280, 25960-25972.  
15789405 T.Mayoral, M.Martínez-Júlvez, I.Pérez-Dorado, J.Sanz-Aparicio, C.Gómez-Moreno, M.Medina, and J.A.Hermoso (2005).
Structural analysis of interactions for complex formation between Ferredoxin-NADP+ reductase and its protein partners.
  Proteins, 59, 592-602.
PDB codes: 1e62 1e63 1e64 1go2 1qgy
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.  
14966111 K.Panda, S.Adak, D.Konas, M.Sharma, and D.J.Stuehr (2004).
A conserved aspartate (Asp-1393) regulates NADPH reduction of neuronal nitric-oxide synthase: implications for catalysis.
  J Biol Chem, 279, 18323-18333.  
12805387 G.M.Knudsen, C.R.Nishida, S.D.Mooney, and P.R.Ortiz de Montellano (2003).
Nitric-oxide synthase (NOS) reductase domain models suggest a new control element in endothelial NOS that attenuates calmodulin-dependent activity.
  J Biol Chem, 278, 31814-31824.  
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
12581212 M.Faro, B.Schiffler, A.Heinz, I.Nogués, M.Medina, R.Bernhardt, and C.Gómez-Moreno (2003).
Insights into the design of a hybrid system between Anabaena ferredoxin-NADP+ reductase and bovine adrenodoxin.
  Eur J Biochem, 270, 726-735.  
12709048 N.Carrillo, and E.A.Ceccarelli (2003).
Open questions in ferredoxin-NADP+ reductase catalytic mechanism.
  Eur J Biochem, 270, 1900-1915.  
12445771 D.D.Boehr, A.R.Farley, G.D.Wright, and J.R.Cox (2002).
Analysis of the pi-pi stacking interactions between the aminoglycoside antibiotic kinase APH(3')-IIIa and its nucleotide ligands.
  Chem Biol, 9, 1209-1217.  
12372607 J.T.Jarrett, and J.T.Wan (2002).
Thermal inactivation of reduced ferredoxin (flavodoxin):NADP+ oxidoreductase from Escherichia coli.
  FEBS Lett, 529, 237-242.  
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
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.  
12359874 S.Adak, M.Sharma, A.L.Meade, and D.J.Stuehr (2002).
A conserved flavin-shielding residue regulates NO synthase electron transfer and nicotinamide coenzyme specificity.
  Proc Natl Acad Sci U S A, 99, 13516-13521.  
12177066 T.M.Louie, H.Yang, P.Karnchanaphanurach, X.S.Xie, and L.Xun (2002).
FAD is a preferred substrate and an inhibitor of Escherichia coli general NAD(P)H:flavin oxidoreductase.
  J Biol Chem, 277, 39450-39455.  
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.  
11076508 J.K.Hurley, M.Faro, T.B.Brodie, J.T.Hazzard, M.Medina, C.Gómez-Moreno, and G.Tollin (2000).
Highly nonproductive complexes with Anabaena ferredoxin at low ionic strength are induced by nonconservative amino acid substitutions at Glu139 in Anabaena ferredoxin:NADP+ reductase.
  Biochemistry, 39, 13695-13702.  
10744737 L.Piubelli, A.Aliverti, A.K.Arakaki, N.Carrillo, E.A.Ceccarelli, P.A.Karplus, and G.Zanetti (2000).
Competition between C-terminal tyrosine and nicotinamide modulates pyridine nucleotide affinity and specificity in plant ferredoxin-NADP(+) reductase.
  J Biol Chem, 275, 10472-10476.  
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.  
11053838 R.Morales, G.Kachalova, F.Vellieux, M.H.Charon, and M.Frey (2000).
Crystallographic studies of the interaction between the ferredoxin-NADP+ reductase and ferredoxin from the cyanobacterium Anabaena: looking for the elusive ferredoxin molecule.
  Acta Crystallogr D Biol Crystallogr, 56, 1408-1412.
PDB code: 1ewy
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
  10493573 J.J.Tanner, S.C.Tu, L.J.Barbour, C.L.Barnes, and K.L.Krause (1999).
Unusual folded conformation of nicotinamide adenine dinucleotide bound to flavin reductase P.
  Protein Sci, 8, 1725-1732.
PDB code: 2bkj
  10452605 J.K.Hurley, J.T.Hazzard, M.Martínez-Júlvez, M.Medina, C.Gómez-Moreno, and G.Tollin (1999).
Electrostatic forces involved in orienting Anabaena ferredoxin during binding to Anabaena ferredoxin:NADP+ reductase: site-specific mutagenesis, transient kinetic measurements, and electrostatic surface potentials.
  Protein Sci, 8, 1614-1622.  
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
10625442 R.Morales, M.H.Charon, G.Hudry-Clergeon, Y.Pétillot, S.Norager, M.Medina, and M.Frey (1999).
Refined X-ray structures of the oxidized, at 1.3 A, and reduced, at 1.17 A, [2Fe-2S] ferredoxin from the cyanobacterium Anabaena PCC7119 show redox-linked conformational changes.
  Biochemistry, 38, 15764-15773.
PDB codes: 1czp 1qt9
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
9761836 A.Gruez, M.Zeghouf, J.Bertrand, M.Eschenbrenner, J.Covès, M.Fontecave, D.Pignol, and J.C.Fontecilla-Camps (1998).
The FNR-like domain of the Escherichia coli sulfite reductase flavoprotein component: crystallization and preliminary X-ray analysis.
  Acta Crystallogr D Biol Crystallogr, 54, 135-136.  
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.  
9558349 C.M.Jenkins, and M.R.Waterman (1998).
NADPH-flavodoxin reductase and flavodoxin from Escherichia coli: characteristics as a soluble microsomal P450 reductase.
  Biochemistry, 37, 6106-6113.  
  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.  
9545063 P.A.van den Berg, A.van Hoek, C.D.Walentas, R.N.Perham, and A.J.Visser (1998).
Flavin fluorescence dynamics and photoinduced electron transfer in Escherichia coli glutathione reductase.
  Biophys J, 74, 2046-2058.  
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.  
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.  
  9416602 D.M.Hoover, and M.L.Ludwig (1997).
A flavodoxin that is required for enzyme activation: the structure of oxidized flavodoxin from Escherichia coli at 1.8 A resolution.
  Protein Sci, 6, 2525-2537.
PDB codes: 1ag9 1ahn
9287153 J.K.Hurley, A.M.Weber-Main, M.T.Stankovich, M.M.Benning, J.B.Thoden, J.L.Vanhooke, H.M.Holden, Y.K.Chae, B.Xia, H.Cheng, J.L.Markley, M.Martinez-Júlvez, C.Gómez-Moreno, J.L.Schmeits, and G.Tollin (1997).
Structure-function relationships in Anabaena ferredoxin: correlations between X-ray crystal structures, reduction potentials, and rate constants of electron transfer to ferredoxin:NADP+ reductase for site-specific ferredoxin mutants.
  Biochemistry, 36, 11100-11117.
PDB codes: 1j7a 1j7b 1j7c 1qob 1qoc 1qod 1qoe 1qof 1qog
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 codes are shown on the right.