PDBsum entry 1a8p

Oxidoreductase

PDB id: 1a8p

Contents

Protein chain

257 a.a. *

Ligands

FAD

Waters ×85

* Residue conservation analysis

PDB id:

1a8p

Name:

Oxidoreductase

Title:

Ferredoxin reductase from azotobacter vinelandii

Structure:

Nadph\:ferredoxin oxidoreductase. Chain: a. Synonym: ferredoxin reductase

Source:

Azotobacter vinelandii. Organism_taxid: 354. Strain: lm100

Resolution:

2.00Å R-factor: 0.206 R-free: 0.262

Authors:

G.S.Prasad,N.Kresge,A.B.Muhlberg,A.Shaw,Y.S.Jung,B.K.Burgess, C.D.Stout

Key ref:

G.Sridhar Prasad et al. (1998). The crystal structure of NADPH:ferredoxin reductase from Azotobacter vinelandii. Protein Sci, 7, 2541-2549. PubMed id: 9865948 DOI: 10.1002/pro.5560071207

Date:

28-Mar-98 Release date: 17-Jun-98

Protein chain

Q44532  (FENR_AZOVI) -  Ferredoxin--NADP reductase from Azotobacter vinelandii

Seq: 258 a.a.

Struc: 257 a.a.

Enzyme reactions

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

reference

DOI no: 10.1002/pro.5560071207

Protein Sci 7:2541-2549 (1998)

PubMed id: 9865948

The crystal structure of NADPH:ferredoxin reductase from Azotobacter vinelandii.

G.Sridhar Prasad, N.Kresge, A.B.Muhlberg, A.Shaw, Y.S.Jung, B.K.Burgess, C.D.Stout.

ABSTRACT

NADPH:ferredoxin reductase (AvFPR) is involved in the response to oxidative stress in Azotobacter vinelandii. The crystal structure of AvFPR has been determined at 2.0 A resolution. The polypeptide fold is homologous with six other oxidoreductases whose structures have been solved including Escherichia coli flavodoxin reductase (EcFldR) and spinach, and Anabaena ferredoxin:NADP+ reductases (FNR). AvFPR is overall most homologous to EcFldR. The structure is comprised of a N-terminal six-stranded antiparallel beta-barrel domain, which binds FAD, and a C-terminal five-stranded parallel beta-sheet domain, which binds NADPH/NADP+ and has a classical nucleotide binding fold. The two domains associate to form a deep cleft where the NADPH and FAD binding sites are juxtaposed. The structure displays sequence conserved motifs in the region surrounding the two dinucleotide binding sites, which are characteristic of the homologous enzymes. The folded over conformation of FAD in AvFPR is similar to that in EcFldR due to stacking of Phe255 on the adenine ring of FAD, but it differs from that in the FNR enzymes, which lack a homologous aromatic residue. The structure of AvFPR displays three unique features in the environment of the bound FAD. Two features may affect the rate of reduction of FAD: the absence of an aromatic residue stacked on the isoalloxazine ring in the NADPH binding site; and the interaction of a carbonyl group with N10 of the flavin. Both of these features are due to the substitution of a conserved C-terminal tyrosine residue with alanine (Ala254) in AvFPR. An additional unique feature may affect the interaction of AvFPR with its redox partner ferredoxin I (FdI). This is the extension of the C-terminus by three residues relative to EcFldR and by four residues relative to FNR. The C-terminal residue, Lys258, interacts with the AMP phosphate of FAD. Consequently, both phosphate groups are paired with a basic group due to the simultaneous interaction of the FMN phosphate with Arg51 in a conserved FAD binding motif. The fourth feature, common to homologous oxidoreductases, is a concentration of 10 basic residues on the face of the protein surrounding the active site, in addition to Arg51 and Lys258.

Selected figure(s)

Figure 2.
Fig. 2. Thepolypeptide fold of AvFF'R withbound FAD. hP-strandsand a-helices of theN-terminal(right)andC-terminaldomains (left) are indicated.

Figure 5.
Fig. 5. Stereofigure of local environment ofFAD in AvFPR showing residues 1-54of the RxYS/T motif, Phe37, residues 252-258, which include a unique C-terminal extension, Cys219 residues 121 of the GT/SGxxP motif. Tyr53 and Phe255 are involved in stacking interactions with the isoalloxazine and adenine rings of respectively. Ala254 is an aromatic residue in the EcFldR and enzymes. Water molecules (crosses) occupy the NADPH binding site adjacent to the flavin. The conserved residues Ser54 Cys219 lie on either side of this cavity. Possible hydrogen bonds are indicated with distances in A. Each phosphate ofFAD interacts with a basic residue and the carbonyl oxygen of Ala254 is adjacent o N10 of the flavin. Not are the residues f the helix a1 whose N-terminal dipole is oriented toward the phosphates, and specific hydrogen bonds between 02 and N3 of flavin and residues on strand 05.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1998, 7, 2541-2549) copyright 1998.

Figures were selected by an automated process.