spacer
spacer

PDBsum entry 1b2r

Go to PDB code: 
protein ligands links
Oxidoreductase PDB id
1b2r
Jmol
Contents
Protein chain
295 a.a. *
Ligands
SO4
FAD
Waters ×657
* Residue conservation analysis
PDB id:
1b2r
Name: Oxidoreductase
Title: Ferredoxin-NADP+ reductase (mutation: e 301 a)
Structure: Protein (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:
1.80Å     R-factor:   0.190     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:
T.Mayoral et al. (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. PubMed id: 10651039 DOI: 10.1002/(SICI)1097-0134(20000101)38:1<60::AID-PROT7>3.3.CO;2-2
Date:
27-Nov-98     Release date:   15-Dec-99    
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: 10.1002/(SICI)1097-0134(20000101)38:1<60::AID-PROT7>3.3.CO;2-2 Proteins 38:60-69 (2000)
PubMed id: 10651039  
 
 
Structural basis of the catalytic role of Glu301 in Anabaena PCC 7119 ferredoxin-NADP+ reductase revealed by x-ray crystallography.
T.Mayoral, M.Medina, J.Sanz-Aparicio, C.Gómez-Moreno, J.A.Hermoso.
 
  ABSTRACT  
 
The three-dimensional crystal structure of the Glu301Ala site-directed mutant of ferredoxin-NADP+ reductase from Anabaena PCC 7119 has been determined at 1.8A resolution by x-ray diffraction. The overall folding of the Glu301Ala FNR mutant shows no significant differences with respect to that of the wild-type enzyme. However, interesting conformational changes are detected in the side chain of another glutamate residue, Glu139, which now points towards the FAD cofactor in the active center cavity. The new conformation of the Glu139 side chain is stabilized by a network of five hydrogen bonds to several water molecules, which seem to hold the carboxylate side chain in a rather fixed position. This interacting network connects the Glu139 side chain to the Ser80 side chain through a series of three water molecules. These observations are discussed in terms of the reactivity of Glu301Ala ferredoxin-NADP+ reductase towards its substrates, and the role of Glu301 in the catalysis is re-examined. Moreover, a structural explanation of the different reoxidation properties of this mutant is given on the basis of the reported structure by modeling the hypothetical flavin C(4a)-hydroperoxide intermediate. The model shows that the distal oxygen of the peroxide anion could be in an appropriate situation to act as the proton donor in the reoxidation process.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. A section of the molecular surface near the FAD group (represented as CPK and seen approximately in the same orientation) in (a) FNR wild-type enzyme and in (b) the Glu301Ala FNR. A new pocket is formed next to the FAD group increasing the solvent accessibility surface by 8 Å.[2] The C4a atom of isoalloxazine ring is highlighted (see Fig. 5 for labeling).
Figure 5.
Figure 5. The flavin-C(4a)-hydroperoxide model. a: Schematic diagram. b: Stereo view of the superposition of the flavin-C(4a)-hydroperoxide model (dashed lines) and the flavin ring of the Glu301Ala FNR structure (solid lines). The arrow indicates the rotation needed to generate the Od allowed region (see text).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2000, 38, 60-69) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
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
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.