PDBsum entry: 1gjr

Oxidoreductase

PDB id: 1gjr

Contents

Protein chain

295 a.a. *

Ligands

FAD

NAP

Waters ×200

* Residue conservation analysis

PDB id:

1gjr

Name:

Oxidoreductase

Title:

Ferredoxin-NADP+ reductase complexed with NADP+ by cocrystallization

Structure:

Ferredoxin-NADP reductase. Chain: a. Fragment: residues 137-440. Synonym: fnr, ferredoxin-NADP+ reductase. Engineered: yes

Source:

Anabaena sp.. Organism_taxid: 1168. Strain: pcc 7119. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.1Å R-factor: 0.200 R-free: 0.270

Authors:

J.A.Hermoso,T.Mayoral,M.Medina,J.Sanz-Aparicio, C.Gomez-Moreno

Key ref:

J.A.Hermoso et al. (2002). Mechanism of coenzyme recognition and binding revealed by crystal structure analysis of ferredoxin-NADP+ reductase complexed with NADP+. J Mol Biol, 319, 1133-1142. PubMed id: 12079352 DOI: 10.1016/S0022-2836(02)00388-1

Date:

01-Aug-01 Release date: 27-Jun-02

Protein chain

P21890  (FENR_ANASO) -  Ferredoxin--NADP reductase

Seq: 440 a.a.

Struc: 295 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.18.1.2 - Ferredoxin--NADP(+) reductase.
• Pathway: Methionine Synthase
• Reaction: 2 reduced ferredoxin + NADP⁺ + H⁺ = 2 oxidized ferredoxin + NADPH

2 × reduced ferredoxin + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) + 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 

• Cellular component: thylakoid membrane (1 term)
• Biological process: oxidation reduction (1 term)
• Biochemical function: oxidoreductase activity (4 terms)

reference

DOI no: 10.1016/S0022-2836(02)00388-1

J Mol Biol 319:1133-1142 (2002)

PubMed id: 12079352

Mechanism of coenzyme recognition and binding revealed by crystal structure analysis of ferredoxin-NADP+ reductase complexed with NADP+.

J.A.Hermoso, T.Mayoral, M.Faro, C.Gómez-Moreno, J.Sanz-Aparicio, M.Medina.

ABSTRACT

The flavoenzyme ferredoxin-NADP+ reductase (FNR) catalyses the production of NADPH in photosynthesis. The three-dimensional structure of FNR presents two distinct domains, one for binding of the FAD prosthetic group and the other for NADP+ binding. In spite of extensive experiments and different crystallographic approaches, many aspects about how the NADP+ substrate binds to FNR and how the hydride ion is transferred from FAD to NADP+ remain unclear. The structure of an FNR:NADP+ complex from Anabaena has been determined by X-ray diffraction analysis of the cocrystallised units to 2.1 A resolution. Structural perturbation of FNR induced by complex formation produces a narrower cavity in which the 2'-phospho-AMP and pyrophosphate portions of the NADP+ are perfectly bound. In addition, the nicotinamide mononucleotide moiety is placed in a new pocket created near the FAD cofactor with the ribose being in a tight conformation. The crystal structure of this FNR:NADP+ complex obtained by cocrystallisation displays NADP+ in an unusual conformation and can be considered as an intermediate state in the process of coenzyme recognition and binding. Structural analysis and comparison with previously reported complexes allow us to postulate a mechanism which would permit efficient hydride transfer to occur. Besides, this structure gives new insights into the postulated formation of the ferredoxin:FNR:NADP+ ternary complex by prediction of new intermolecular interactions, which could only exist after FNR:NADP+ complex formation. Finally, structural comparison with the members of the broad FNR structural family also provides an explanation for the high specificity exhibited by FNR for NADP+/H versus NAD+/H.

Selected figure(s)

Figure 1.
Figure 1. Overall structure of the FNR:NADP+ complex and enzyme-coenzyme interactions. (a) Ribbon diagram of the FNR:NADP+ complex, with the FAD prosthetic group and NADP+ coenzyme represented as balls and sticks, and the protein-binding domains for each cofactor being coloured in cyan and green, respectively. (b) FNR residues interacting with NADP+ (coloured in green) are represented as ball and sticks. (c) Relative positions of isoalloxazine (orange) and nicotinamide (green) rings in the FNR:NADP+ complex. In spite of the proximity between both rings there is no displacement of Tyr303. This C-terminal Tyr is well stabilised by a stacking interaction with the isoalloxazine ring and by a bifurcated hydrogen bond with a water molecule and Thr157.

Figure 3.
Figure 3. Different NADP+ conformations in the FNR:NADP+ complexes. (a) Superposition of the two NADP+ conformations observed for the different complexes onto the cocrystallised Anabaena FNR:NADP+ structure. Coenzyme conformation obtained by soaking[3.] is coloured in red (complex I), cocrystallised coenzyme is coloured in magenta (complex II) and NADP+ conformation obtained after mutation of the C-terminal Tyr in pea FNR[19.] is coloured in green (complex III). The FAD cofactor is coloured in blue. (b) Superposition of the cocrystallised Anabaena FNR:NADP+ complex (orange) and the pea FNR:NADP+ complex (green). FAD and NADP+ cofactors are coloured in magenta for complex II and in cyan for complex III. Residues interacting with NADP+ in both structures are represented as ball and sticks (see Figure 1(b) for labelling).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 319, 1133-1142) copyright 2002.

Figures were selected by the author.