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PDBsum entry 1gaq

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protein ligands Protein-protein interface(s) links
Oxidoreductase/electron transport PDB id
1gaq
Jmol
Contents
Protein chains
296 a.a. *
98 a.a. *
Ligands
FAD ×2
FES
Waters ×133
* Residue conservation analysis
PDB id:
1gaq
Name: Oxidoreductase/electron transport
Title: Crystal structure of the complex between ferredoxin and ferredoxin-NADP+ reductase
Structure: Ferredoxin-NADP+ reductase. Chain: a, c. Synonym: fnr. Engineered: yes. Ferredoxin i. Chain: b. Synonym: fd. Engineered: yes
Source: Zea mays. Organism_taxid: 4577. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Monomer (from PQS)
Resolution:
2.59Å     R-factor:   0.232     R-free:   0.297
Authors: G.Kurisu,M.Kusunoki,T.Hase
Key ref:
G.Kurisu et al. (2001). Structure of the electron transfer complex between ferredoxin and ferredoxin-NADP(+) reductase. Nat Struct Biol, 8, 117-121. PubMed id: 11175898 DOI: 10.1038/84097
Date:
08-May-00     Release date:   07-Feb-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9SLP6  (Q9SLP6_MAIZE) -  Ferredoxin
Seq:
Struc:
355 a.a.
296 a.a.
Protein chain
Pfam   ArchSchema ?
P27787  (FER1_MAIZE) -  Ferredoxin-1, chloroplastic
Seq:
Struc:
150 a.a.
98 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     electron carrier activity     4 terms  

 

 
DOI no: 10.1038/84097 Nat Struct Biol 8:117-121 (2001)
PubMed id: 11175898  
 
 
Structure of the electron transfer complex between ferredoxin and ferredoxin-NADP(+) reductase.
G.Kurisu, M.Kusunoki, E.Katoh, T.Yamazaki, K.Teshima, Y.Onda, Y.Kimata-Ariga, T.Hase.
 
  ABSTRACT  
 
All oxygenic photosynthetically derived reducing equivalents are utilized by combinations of a single multifuctional electron carrier protein, ferredoxin (Fd), and several Fd-dependent oxidoreductases. We report the first crystal structure of the complex between maize leaf Fd and Fd-NADP(+) oxidoreductase (FNR). The redox centers in the complex--the 2Fe-2S cluster of Fd and flavin adenine dinucleotide (FAD) of FNR--are in close proximity; the shortest distance is 6.0 A. The intermolecular interactions in the complex are mainly electrostatic, occurring through salt bridges, and the interface near the prosthetic groups is hydrophobic. NMR experiments on the complex in solution confirmed the FNR recognition sites on Fd that are identified in the crystal structure. Interestingly, the structures of Fd and FNR in the complex and in the free state differ in several ways. For example, in the active site of FNR, Fd binding induces the formation of a new hydrogen bond between side chains of Glu 312 and Ser 96 of FNR. We propose that this type of molecular communication not only determines the optimal orientation of the two proteins for electron transfer, but also contributes to the modulation of the enzymatic properties of FNR.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structures of the Fd -FNR complex and PDR. a, Stereo view of the maize leaf Fd -FNR complex. The ribbon diagram of FNR is colored blue to yellow along the sequence from the N-terminus to the C-terminus and that of Fd is colored yellow to red. The prosthetic groups, FAD and the 2Fe -2S cluster, and amino acid residues located at the interface are drawn as ball-and-stick models. The residues of FNR are Asn 30, Lys 33, Pro 34, Lys 35, Ser 75, Asp 84, Lys 85, Asn 86, Lys 88, Lys 91, Val 92, Leu 94, Val 151, Gly 152, Lys 153, Glu 154, Glu 278, Phe 297, Lys 301, Lys 304, Arg 305, Val 311, Glu 312, Val 313 and Tyr 314. Those of Fd are Glu 29, Glu 30, Gly 32, Asp 34, Tyr 37, Ser 38, Cys 39, Arg 40, Ala 41, Ser 43, Cys 44, Ser 59, Asp 60, Gln 61, Ser 62, Tyr 63, Leu 64, Asp 65, Asp 66, His 78, Gly 97 and Ala 98. b, Stereo view of Pseudomonas cepacia PDR (PDB code 2PIA) in the same orientation as the Fd -FNR complex. The ribbon diagram is colored blue to yellow for the NAD^+ and FNM domains and yellow to red for the Fe -S domain. FAD and the 2Fe -2S cluster are drawn as ball-and-stick models. All the figures in this paper were generated using Bobscript30 and RENDER from the Raster3D package^31.
Figure 2.
Figure 2. Structure of the interface of the Fd -FNR complex. a, Stereo view of the final -weighted 2F[o] - F[c] electron density map around the two prosthetic groups. Amino acid residues of FNR and Fd are colored black and red, respectively. b, Stereo view of the electrostatic interaction sites at the interface. Amino acid residues forming intermolecular salt bridges are drawn as ball-and-stick models. The distances for salt bridged residue pairs are: Glu 29 OE2 -Lys 304 NZ, 3.88 ┼; Arg 40 NH1 -Glu 154 OE1, 3.33 ┼; Asp 60 OD1 -Lys 33 NZ, 4.51 ┼; Asp 65 OD2 -Lys 91 NZ, 2.80 ┼; Asp 66 OD1 -Lys 88 NZ, 4.16 ┼. c, Structure of spinach Fd (PDB code 1A70). The evolutionarily conserved Glu 29 and Arg 40 are drawn as ball-and-stick models and the salt bridges between them are shown with dotted lines.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 117-121) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21280774 R.Pandey, S.Ghosh, S.Mukhopadhyay, S.Ramasesha, and P.K.Das (2011).
Geometry and quadratic nonlinearity of charge transfer complexes in solution using depolarized hyper-Rayleigh scattering.
  J Chem Phys, 134, 044533.  
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
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
20214498 K.Motohashi, and T.Hisabori (2010).
CcdA is a thylakoid membrane protein required for the transfer of reducing equivalents from stroma to thylakoid lumen in the higher plant chloroplast.
  Antioxid Redox Signal, 13, 1169-1176.  
20111687 A.Brown (2009).
Analysis of cooperativity by isothermal titration calorimetry.
  Int J Mol Sci, 10, 3457-3477.  
19122206 J.Yeom, C.O.Jeon, E.L.Madsen, and W.Park (2009).
In vitro and in vivo interactions of ferredoxin-NADP+ reductases in Pseudomonas putida.
  J Biochem, 145, 481-491.  
19527656 M.Martínez-Júlvez, M.Medina, and A.Velázquez-Campoy (2009).
Binding thermodynamics of ferredoxin:NADP+ reductase: two different protein substrates and one energetics.
  Biophys J, 96, 4966-4975.  
19583765 M.Medina (2009).
Structural and mechanistic aspects of flavoproteins: photosynthetic electron transfer from photosystem I to NADP+.
  FEBS J, 276, 3942-3958.  
19846550 M.Winkler, S.Kuhlgert, M.Hippler, and T.Happe (2009).
Characterization of the key step for light-driven hydrogen evolution in green algae.
  J Biol Chem, 284, 36620-36627.  
19243237 T.Senda, M.Senda, S.Kimura, and T.Ishida (2009).
Redox control of protein conformation in flavoproteins.
  Antioxid Redox Signal, 11, 1741-1766.  
18621810 H.Long, C.H.Chang, P.W.King, M.L.Ghirardi, and K.Kim (2008).
Brownian dynamics and molecular dynamics study of the association between hydrogenase and ferredoxin from Chlamydomonas reinhardtii.
  Biophys J, 95, 3753-3766.  
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.  
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.  
  18323604 N.Muraki, D.Seo, T.Shiba, T.Sakurai, and G.Kurisu (2008).
Crystallization and preliminary X-ray studies of ferredoxin-NAD(P)+ reductase from Chlorobium tepidum.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 186-189.  
18658149 S.L.Tu, H.C.Chen, and L.W.Ku (2008).
Mechanistic Studies of the Phytochromobilin Synthase HY2 from Arabidopsis.
  J Biol Chem, 283, 27555-27564.  
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
17660315 C.H.Chang, P.W.King, M.L.Ghirardi, and K.Kim (2007).
Atomic resolution modeling of the ferredoxin:[FeFe] hydrogenase complex from Chlamydomonas reinhardtii.
  Biophys J, 93, 3034-3045.  
17636129 G.Hagelueken, L.Wiehlmann, T.M.Adams, H.Kolmar, D.W.Heinz, B.Tümmler, and W.D.Schubert (2007).
Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa.
  Proc Natl Acad Sci U S A, 104, 12276-12281.
PDB codes: 2v3a 2v3b
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.  
  17554177 M.Senda, S.Kishigami, S.Kimura, and T.Senda (2007).
Crystallization and preliminary X-ray analysis of the electron-transfer complex of Rieske-type [2Fe-2S] ferredoxin and NADH-dependent ferredoxin reductase derived from Acidovorax sp. strain KKS102.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 520-523.  
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.  
  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.  
16669773 N.Nelson, and C.F.Yocum (2006).
Structure and function of photosystems I and II.
  Annu Rev Plant Biol, 57, 521-565.  
16327013 S.L.Tu, W.Sughrue, R.D.Britt, and J.C.Lagarias (2006).
A conserved histidine-aspartate pair is required for exovinyl reduction of biliverdin by a cyanobacterial phycocyanobilin:ferredoxin oxidoreductase.
  J Biol Chem, 281, 3127-3136.  
16469743 T.Saitoh, T.Ikegami, M.Nakayama, K.Teshima, H.Akutsu, and T.Hase (2006).
NMR study of the electron transfer complex of plant ferredoxin and sulfite reductase: mapping the interaction sites of ferredoxin.
  J Biol Chem, 281, 10482-10488.  
16143852 A.Suzuki, and D.B.Knaff (2005).
Glutamate synthase: structural, mechanistic and regulatory properties, and role in the amino acid metabolism.
  Photosynth Res, 83, 191-217.  
15513928 G.Kurisu, D.Nishiyama, M.Kusunoki, S.Fujikawa, M.Katoh, G.T.Hanke, T.Hase, and K.Teshima (2005).
A structural basis of Equisetum arvense ferredoxin isoform II producing an alternative electron transfer with ferredoxin-NADP+ reductase.
  J Biol Chem, 280, 2275-2281.
PDB code: 1wri
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.  
16038609 N.V.Strushkevich, T.N.Azeva, G.I.Lepesheva, and S.A.Usanov (2005).
Role of positively charged residues lys267, lys270, and arg411 of cytochrome p450scc (CYP11A1) in interaction with adrenodoxin.
  Biochemistry (Mosc), 70, 664-671.  
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
  16511100 Y.Ashikawa, Z.Fujimoto, H.Noguchi, H.Habe, T.Omori, H.Yamane, and H.Nojiri (2005).
Crystallization and preliminary X-ray diffraction analysis of the electron-transfer complex between the terminal oxygenase component and ferredoxin in the Rieske non-haem iron oxygenase system carbazole 1,9a-dioxygenase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 577-580.  
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.  
14613937 J.L.Blazyk, and S.J.Lippard (2004).
Domain engineering of the reductase component of soluble methane monooxygenase from Methylococcus capsulatus (Bath).
  J Biol Chem, 279, 5630-5640.  
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.  
15573135 N.Nelson, and A.Ben-Shem (2004).
The complex architecture of oxygenic photosynthesis.
  Nat Rev Mol Cell Biol, 5, 971-982.  
15103624 P.B.Crowley, and M.A.Carrondo (2004).
The architecture of the binding site in redox protein complexes: implications for fast dissociation.
  Proteins, 55, 603-612.  
12890025 K.Mazouni, F.Domain, F.Chauvat, and C.Cassier-Chauvat (2003).
Expression and regulation of the crucial plant-like ferredoxin of cyanobacteria.
  Mol Microbiol, 49, 1019-1029.  
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.  
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
11872744 M.Maeda, D.Hamada, M.Hoshino, Y.Onda, T.Hase, and Y.Goto (2002).
Partially folded structure of flavin adenine dinucleotide-depleted ferredoxin-NADP+ reductase with residual NADP+ binding domain.
  J Biol Chem, 277, 17101-17107.  
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.  
12324399 P.Fromme, H.Bottin, N.Krauss, and P.Sétif (2002).
Crystallization and electron paramagnetic resonance characterization of the complex of photosystem I with its natural electron acceptor ferredoxin.
  Biophys J, 83, 1760-1773.  
12370173 V.Pandini, G.Caprini, N.Thomsen, A.Aliverti, F.Seeber, and G.Zanetti (2002).
Ferredoxin-NADP+ reductase and ferredoxin of the protozoan parasite Toxoplasma gondii interact productively in Vitro and in Vivo.
  J Biol Chem, 277, 48463-48471.  
11500872 M.Merkx, D.A.Kopp, M.H.Sazinsky, J.L.Blazyk, J.Müller, and S.J.Lippard (2001).
Dioxygen Activation and Methane Hydroxylation by Soluble Methane Monooxygenase: A Tale of Two Irons and Three Proteins A list of abbreviations can be found in Section 7.
  Angew Chem Int Ed Engl, 40, 2782-2807.  
11369223 M.R.Jones, and P.K.Fyfe (2001).
Photosynthesis: new light on biological oxygen production.
  Curr Biol, 11, R318-R321.  
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.