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PDBsum entry 2ok7

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2ok7
Jmol
Contents
Protein chains
262 a.a. *
262 a.a. *
Ligands
FAD ×6
A2P ×6
Metals
_NA
Waters ×228
* Residue conservation analysis
PDB id:
2ok7
Name: Oxidoreductase
Title: Ferredoxin-NADP+ reductase from plasmodium falciparum with 2'p-amp
Structure: Putative ferredoxin--NADP reductase. Chain: a, b, c, d, e, f. Synonym: ferredoxin--NADP reductase, putative. Engineered: yes
Source: Plasmodium falciparum 3d7. Organism_taxid: 36329. Strain: isolate 3d7. Gene: orf pff1115w. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.70Å     R-factor:   0.263     R-free:   0.321
Authors: M.Milani,E.Mastrangelo,M.Bolognesi
Key ref:
M.Milani et al. (2007). Ferredoxin-NADP+ reductase from Plasmodium falciparum undergoes NADP+-dependent dimerization and inactivation: functional and crystallographic analysis. J Mol Biol, 367, 501-513. PubMed id: 17258767 DOI: 10.1016/j.jmb.2007.01.005
Date:
16-Jan-07     Release date:   13-Feb-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
C6KT68  (C6KT68_PLAF7) -  Ferredoxin NADP reductase
Seq:
Struc:
371 a.a.
262 a.a.
Protein chains
Pfam   ArchSchema ?
C6KT68  (C6KT68_PLAF7) -  Ferredoxin NADP reductase
Seq:
Struc:
371 a.a.
262 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, D, E, F: 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: 10.1016/j.jmb.2007.01.005 J Mol Biol 367:501-513 (2007)
PubMed id: 17258767  
 
 
Ferredoxin-NADP+ reductase from Plasmodium falciparum undergoes NADP+-dependent dimerization and inactivation: functional and crystallographic analysis.
M.Milani, E.Balconi, A.Aliverti, E.Mastrangelo, F.Seeber, M.Bolognesi, G.Zanetti.
 
  ABSTRACT  
 
The completion of the Plasmodium falciparum genome sequence has recently promoted the search for new antimalarial drugs. More specifically, metabolic pathways of the apicoplast, a key organelle for survival of the parasite, have been recognized as potential targets for the development of specific new antimalarial agents. As most apicomplexan parasites, P. falciparum displays a plant-type ferredoxin-NADP(+) reductase, yielding reduced ferredoxin for essential biosynthetic pathways in the apicoplast. Here we report a molecular, kinetic and ligand binding characterization of the recombinant ferredoxin-NADP(+) reductase from P. falciparum, in the light of current data available for plant ferredoxin-NADP(+) reductases. In parallel with the functional characterization, we describe the crystal structures of P. falciparum ferredoxin-NADP(+) reductase in free form and in complex with 2'-phospho-AMP (at 2.4 and 2.7 A resolution, respectively). The enzyme displays structural properties likely to be unique to plasmodial reductases. In particular, the two crystal structures highlight a covalent dimer, which relies on the oxidation of residue Cys99 in two opposing subunits, and a helix-coil transition that occurs in the NADP-binding domain, triggered by 2'-phospho-AMP binding. Studies in solution show that NADP(+), as well as 2'-phospho-AMP, promotes the formation of the disulfide-stabilized dimer. The isolated dimer is essentially inactive, but full activity is recovered upon disulfide reduction. The occurrence of residues unique to the plasmodial enzyme, and the discovery of specific conformational properties, highlight the NADP-binding domain of P. falciparum ferredoxin-NADP(+) reductase as particularly suited for the rational development of antimalarial compounds.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Tertiary/quaternary structures in PfFNR and its 2′P-AMP complex. (a) The structure of one isolated chain of PfFNR (inhibitor-free, yellow ribbon) is overlaid on the structure of PfFNR/2′P-AMP (blue ribbon). The bound FAD (left) and 2′P-AMP (right) molecules are displayed as stick models. The lower right part of (a) highlights the conformational helix–coil transition occurring at the β9-αF loop, in the NADP^+ domain, in the absence of the nucleotide. (b) (drawn in the same orientation as (a)) The PfFNR/2′P-AMP polypeptide chain (monomer), color coded for the atomic B-factors; red shows the highest temperature factors (B = 60 Å^2), blue the lowest (B = 10 Å^2). The FAD domain is on the left and the NADP^+ binding domain on the right. FAD and 2′P-AMP are displayed as cyan/red stick models. Note several interrupted segments on the protein surface, corresponding to regions of poor electron density. (c) View of the quaternary assembly observed in the crystal asymmetric unit of PfFNR. The four protein chains are shown in yellow, violet, orange and green, respectively, displaying their respective FAD bound species as stick models. (d) View of the dimeric assembly observed for the disulfide-stabilized PfFNR. The two protein chains are shown in yellow and green, respectively, displaying their respective FAD bound species as stick models. The yellow PfFNR subunit has the same orientation adopted in (a) and (b) (two FAD groups are on the left hand side). The Cys99 disulfide, drawn in yellow, is labelled within a square window. (e) Stereo view of the covalent PfFNR/2′P-AMP dimer. The two PfFNR molecules are shown in blue and orange, respectively. The Cys99 disulfide is highlighted by a square box, and labelled. Two FAD molecules are shown as yellow stick models; 2′P-AMP stick models are in cyan. The blue subunit has the same orientation of the protein chain in (a) and (b). Figure 3. Tertiary/quaternary structures in PfFNR and its 2′P-AMP complex. (a) The structure of one isolated chain of PfFNR (inhibitor-free, yellow ribbon) is overlaid on the structure of PfFNR/2′P-AMP (blue ribbon). The bound FAD (left) and 2′P-AMP (right) molecules are displayed as stick models. The lower right part of (a) highlights the conformational helix–coil transition occurring at the β9-αF loop, in the NADP^+ domain, in the absence of the nucleotide. (b) (drawn in the same orientation as (a)) The PfFNR/2′P-AMP polypeptide chain (monomer), color coded for the atomic B-factors; red shows the highest temperature factors (B = 60 Å^2), blue the lowest (B = 10 Å^2). The FAD domain is on the left and the NADP^+ binding domain on the right. FAD and 2′P-AMP are displayed as cyan/red stick models. Note several interrupted segments on the protein surface, corresponding to regions of poor electron density. (c) View of the quaternary assembly observed in the crystal asymmetric unit of PfFNR. The four protein chains are shown in yellow, violet, orange and green, respectively, displaying their respective FAD bound species as stick models. (d) View of the dimeric assembly observed for the disulfide-stabilized PfFNR. The two protein chains are shown in yellow and green, respectively, displaying their respective FAD bound species as stick models. The yellow PfFNR subunit has the same orientation adopted in (a) and (b) (two FAD groups are on the left hand side). The Cys99 disulfide, drawn in yellow, is labelled within a square window. (e) Stereo view of the covalent PfFNR/2′P-AMP dimer. The two PfFNR molecules are shown in blue and orange, respectively. The Cys99 disulfide is highlighted by a square box, and labelled. Two FAD molecules are shown as yellow stick models; 2′P-AMP stick models are in cyan. The blue subunit has the same orientation of the protein chain in (a) and (b).
Figure 4.
Figure 4. Electrostatics at the PfFNR NADP^+ binding site. (a) A mono view of the enzyme surface, colour coded for the distribution of electrostatic charges, around the 2′P-AMP (the lower green stick model in the Figure; the 2′ and 5′ phosphate groups are labelled), and the FAD binding sites (the overall orientation of the protein is close to that of Figure 3(a) and (b)). A lack of positive charge around the 2′ phosphate group is evident, if just one PfFNR/2′P-AMP subunit is considered, as in this Figure. (b) When the PfFNR/2′P-AMP dimer is assembled, the electrostatic contribution of residues provided by the opposing subunit becomes evident around the 2′ phosphate group of the inhibitor, as shown by the wider distribution of positive electrostatic charge (blue colour). Part of the secondary structure building the NADP^+ binding domain is shown as cyan ribbons (colour code: red, −10 kT/e; white, 0 kT/e; blue, 10 kT/e). Figure 4. Electrostatics at the PfFNR NADP^+ binding site. (a) A mono view of the enzyme surface, colour coded for the distribution of electrostatic charges, around the 2′P-AMP (the lower green stick model in the Figure; the 2′ and 5′ phosphate groups are labelled), and the FAD binding sites (the overall orientation of the protein is close to that of [3]Figure 3(a) and (b)). A lack of positive charge around the 2′ phosphate group is evident, if just one PfFNR/2′P-AMP subunit is considered, as in this Figure. (b) When the PfFNR/2′P-AMP dimer is assembled, the electrostatic contribution of residues provided by the opposing subunit becomes evident around the 2′ phosphate group of the inhibitor, as shown by the wider distribution of positive electrostatic charge (blue colour). Part of the secondary structure building the NADP^+ binding domain is shown as cyan ribbons (colour code: red, −10 kT/e; white, 0 kT/e; blue, 10 kT/e).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 367, 501-513) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20737579 C.Lei, S.D.Rider, C.Wang, H.Zhang, X.Tan, and G.Zhu (2010).
The apicomplexan Cryptosporidium parvum possesses a single mitochondrial-type ferredoxin and ferredoxin:NADP+ reductase system.
  Protein Sci, 19, 2073-2084.  
  19768685 J.R.Gallagher, and S.T.Prigge (2010).
Plasmodium falciparum acyl carrier protein crystal structures in disulfide-linked and reduced states and their prevalence during blood stage growth.
  Proteins, 78, 575-588.
PDB codes: 3gzl 3gzm
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.  
19237441 K.Singh, and V.Bhakuni (2009).
Guanidine hydrochloride- and urea-induced unfolding of Toxoplasma gondii ferredoxin-NADP+ reductase: stabilization of a functionally inactive holo-intermediate.
  J Biochem, 145, 721-731.  
18410491 G.T.Hanke, T.Endo, F.Satoh, and T.Hase (2008).
Altered photosynthetic electron channelling into cyclic electron flow and nitrite assimilation in a mutant of ferredoxin:NADP(H) reductase.
  Plant Cell Environ, 31, 1017-1028.  
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.  
18175327 K.Singh, and V.Bhakuni (2008).
Toxoplasma gondii ferredoxin-NADP+ reductase: Role of ionic interactions in stabilization of native conformation and structural cooperativity.
  Proteins, 71, 1879-1888.  
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
17635583 M.de Rosa, A.Pennati, V.Pandini, E.Monzani, G.Zanetti, and A.Aliverti (2007).
Enzymatic oxidation of NADP+ to its 4-oxo derivative is a side-reaction displayed only by the adrenodoxin reductase type of ferredoxin-NADP+ reductases.
  FEBS J, 274, 3998-4007.  
17875391 P.Gayathri, H.Balaram, and M.R.Murthy (2007).
Structural biology of plasmodial proteins.
  Curr Opin Struct Biol, 17, 744-754.  
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.