PDBsum entry 1ddi

Oxidoreductase

PDB id: 1ddi

Contents

Protein chain

374 a.a. *

Ligands

FAD

NAP

Waters ×271

* Residue conservation analysis

PDB id:

1ddi

Name:

Oxidoreductase

Title:

Crystal structure of sir-fp60

Structure:

Sulfite reductase [nadph] flavoprotein alpha-component. Chain: a. Fragment: sir-fp60. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.51Å R-factor: 0.185 R-free: 0.245

Authors:

A.Gruez,D.Pignol,M.Zeghouf,J.Coves,M.Fontecave,J.L.Ferrer, J.C.Fontecilla-Camps

Key ref:

A.Gruez et al. (2000). Four crystal structures of the 60 kDa flavoprotein monomer of the sulfite reductase indicate a disordered flavodoxin-like module. J Mol Biol, 299, 199-212. PubMed id: 10860732 DOI: 10.1006/jmbi.2000.3748

Date:

10-Nov-99 Release date: 13-Nov-00

Protein chain

P38038  (CYSJ_ECOLI) -  Sulfite reductase [NADPH] flavoprotein alpha-component from Escherichia coli (strain K12)

Seq: 599 a.a.

Struc: 374 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.8.1.2 - assimilatory sulfite reductase (NADPH).
• Reaction: hydrogen sulfide + 3 NADP⁺ + 3 H2O = sulfite + 3 NADPH + 4 H⁺
• Cofactor: FAD; FMN; Iron-sulfur; Siroheme

FAD (Bound ligand (Het Group name = FAD) corresponds exactly) FMN Iron-sulfur Siroheme

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1006/jmbi.2000.3748

J Mol Biol 299:199-212 (2000)

PubMed id: 10860732

Four crystal structures of the 60 kDa flavoprotein monomer of the sulfite reductase indicate a disordered flavodoxin-like module.

A.Gruez, D.Pignol, M.Zeghouf, J.Covès, M.Fontecave, J.L.Ferrer, J.C.Fontecilla-Camps.

ABSTRACT

Escherichia coli NADPH-sulfite reductase (SiR) is a 780 kDa multimeric hemoflavoprotein composed of eight alpha-subunits (SiR-FP) and four beta-subunits (SiR-HP) that catalyses the six electron reduction of sulfite to sulfide. Each beta-subunit contains a Fe4S4 cluster and a siroheme, and each alpha-subunit binds one FAD and one FMN as prosthetic groups. The FAD gets electrons from NADPH, and the FMN transfers the electrons to the metal centers of the beta-subunit for sulfite reduction. We report here the 1.94 A X-ray structure of SiR-FP60, a recombinant monomeric fragment of SiR-FP that binds both FAD and FMN and retains the catalytic properties of the native protein. The structure can be divided into three domains. The carboxy-terminal part of the enzyme is composed of an antiparallel beta-barrel which binds the FAD, and a variant of the classical pyridine dinucleotide binding fold which binds NADPH. These two domains form the canonic FNR-like module, typical of the ferredoxin NADP+ reductase family. By analogy with the structure of the cytochrome P450 reductase, the third domain, composed of seven alpha-helices, is supposed to connect the FNR-like module to the N-terminal flavodoxine-like module. In four different crystal forms, the FMN-binding module is absent from electron density maps, although mass spectroscopy, amino acid sequencing and activity experiments carried out on dissolved crystals indicate that a functional module is present in the protein. Our results clearly indicate that the interaction between the FNR-like and the FMN-like modules displays lower affinity than in the case of cytochrome P450 reductase. The flexibility of the FMN-binding domain may be related, as observed in the case of cytochrome bc1, to a domain reorganisation in the course of electron transfer. Thus, a movement of the FMN-binding domain relative to the rest of the enzyme may be a requirement for its optimal positioning relative to both the FNR-like module and the beta-subunit.

Selected figure(s)

Figure 1.
Figure 1. Ribbon diagram of SiR- FP60 produced with the program MOLSCRIPT (Kraulis, 1991) and Render 3D (Merrit & Bacon, 1997). The colors vary from blue for the N-terminal residue to red for the C-terminal residue. Cofactors are represented by balls and sticks.

Figure 7.
Figure 7. Electrostatic potential surfaces of SiR-FP60 and cytochrome P450 reductase (CPR). (a) The relative orien- tations of the FMN-binding domain (gold) and the FNR-like module (silver) in CPR. The electrostatic potential sur- faces of the FNR-like module of CPR (b) and of SiR-FP60 (c) are depicted in the same orientation as in (a). The complementary surface of the FMN-binding domain of CPR (d) and of a model of the equivalent region of SiR-FP60 (e) are shown in the side opposite to (a), obtained by 180 ° rotation about the y-axis. SiR-FP60 FMN-binding domain was modeled using the CPR coordinates,with the program Modeller (Sali & Blundell, 1993). The Figure was prepared with the program Grasp (Nicholls et al., 1991).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 299, 199-212) copyright 2000.

Figures were selected by an automated process.