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PDBsum entry 1bqe

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Oxidoreductase PDB id
1bqe
Jmol
Contents
Protein chain
295 a.a. *
Ligands
SO4
FAD
Waters ×267
* Residue conservation analysis
PDB id:
1bqe
Name: Oxidoreductase
Title: Ferredoxin:nadp+ reductase mutant with thr 155 replaced by g
Structure: Ferredoxin--NADP reductase. Chain: a. Synonym: fnr. Engineered: yes. Mutation: yes
Source: Nostoc sp.. Organism_taxid: 1168. Strain: pcc 7119. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.45Å     R-factor:   0.160     R-free:   0.240
Authors: J.A.Hermoso,T.Mayoral,M.Medina,M.Martinez-Ripoll,M.Martinez- J.Sanz-Aparicio,C.Gomez-Moreno
Key ref:
M.Medina et al. (2001). Probing the determinants of coenzyme specificity in ferredoxin-NADP+ reductase by site-directed mutagenesis. J Biol Chem, 276, 11902-11912. PubMed id: 11152461 DOI: 10.1074/jbc.M009287200
Date:
14-Aug-98     Release date:   27-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21890  (FENR_ANASO) -  Ferredoxin--NADP reductase
Seq:
Struc:
440 a.a.
295 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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: 10.1074/jbc.M009287200 J Biol Chem 276:11902-11912 (2001)
PubMed id: 11152461  
 
 
Probing the determinants of coenzyme specificity in ferredoxin-NADP+ reductase by site-directed mutagenesis.
M.Medina, A.Luquita, J.Tejero, J.Hermoso, T.Mayoral, J.Sanz-Aparicio, K.Grever, C.Gomez-Moreno.
 
  ABSTRACT  
 
On the basis of sequence and three-dimensional structure comparison between Anabaena PCC7119 ferredoxin-NADP(+) reductase (FNR) and other reductases from its structurally related family that bind either NADP(+)/H or NAD(+)/H, a set of amino acid residues that might determine the FNR coenzyme specificity can be assigned. These residues include Thr-155, Ser-223, Arg-224, Arg-233 and Tyr-235. Systematic replacement of these amino acids was done to identify which of them are the main determinants of coenzyme specificity. Our data indicate that all of the residues interacting with the 2'-phosphate of NADP(+)/H in Anabaena FNR are not involved to the same extent in determining coenzyme specificity and affinity. Thus, it is found that Ser-223 and Tyr-235 are important for determining NADP(+)/H specificity and orientation with respect to the protein, whereas Arg-224 and Arg-233 provide only secondary interactions in Anabaena FNR. The analysis of the T155G FNR form also indicates that the determinants of coenzyme specificity are not only situated in the 2'-phosphate NADP(+)/H interacting region but that other regions of the protein must be involved. These regions, although not interacting directly with the coenzyme, must produce specific structural arrangements of the backbone chain that determine coenzyme specificity. The loop formed by residues 261-268 in Anabaena FNR must be one of these regions.
 
  Selected figure(s)  
 
Figure 9.
Fig. 9. Hydrogen bond network and structural differences in the FNR WT (A) and in the T155G FNR mutant (B). In the native state, OH (Thr-155) is making a bifurcated H-bond with the Leu-263 residue. Two new interactions are created after mutation: O (Leu-263) stabilizes a new interaction with N (Met-266), and O 2 (Gly-267) stabilizes a new interaction with N (Gly-265). This produces a less extended conformation for the 261-268 loop in the mutated enzyme.
Figure 10.
Fig. 10. MOLSCRIPT drawing of the superposition of Anabaena FNR (light) and NADH-cytochrome b[5] reductase (dark) (58) near the position of residue 155. In the NAD^+/H-dependent enzymes, a Gly residue at this position is favored due to the presence of a hairpin-like region (formed by a series of prolines) that will not allow the space for a Thr to occupy position 155 of FNR. On the contrary, the absence of this hairpin in the NADP+/H-dependent enzymes permits the presence of residues such as Thr or Pro at this position. Relevant residues are labeled as chain A in FNR or chain B in cytochrome b[5] reductase.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 11902-11912) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19693930 G.A.Khoury, H.Fazelinia, J.W.Chin, R.J.Pantazes, P.C.Cirino, and C.D.Maranas (2009).
Computational design of Candida boidinii xylose reductase for altered cofactor specificity.
  Protein Sci, 18, 2125-2138.  
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
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.  
12450807 J.W.Nam, H.Nojiri, H.Noguchi, H.Uchimura, T.Yoshida, H.Habe, H.Yamane, and T.Omori (2002).
Purification and characterization of carbazole 1,9a-dioxygenase, a three-component dioxygenase system of Pseudomonas resinovorans strain CA10.
  Appl Environ Microbiol, 68, 5882-5890.  
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
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.