PDBsum entry 1d4d

Oxidoreductase

PDB id: 1d4d

Contents

Protein chain

560 a.a. *

Ligands

HEC ×4

FAD

SIN

Waters ×56

* Residue conservation analysis

PDB id:

1d4d

Name:

Oxidoreductase

Title:

Crystal structure of the succinate complexed form of the flavocytochromE C fumarate reductase of shewanella putrefaciens strain mr-1

Structure:

FlavocytochromE C fumarate reductase. Chain: a. Ec: 1.3.99.1

Source:

Shewanella oneidensis. Organism_taxid: 70863. Strain: mr-1

Resolution:

2.50Å R-factor: 0.239 R-free: 0.305

Authors:

D.Leys,A.S.Tsapin,T.E.Meyer,M.A.Cusanovich,J.J.Van Beeumen

Key ref:

D.Leys et al. (1999). Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1. Nat Struct Biol, 6, 1113-1117. PubMed id: 10581551 DOI: 10.1038/70051

Date:

03-Oct-99 Release date: 01-Dec-99

Protein chain

P83223  (FRDA_SHEON) -  Fumarate reductase (cytochrome) from Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)

Seq: 596 a.a.

Struc: 560 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.1.3.2.4 - fumarate reductase (cytochrome).
• Reaction: 2 Fe(III)-[cytochrome c] + succinate = fumarate + 2 Fe(II)-[cytochrome c] + 2 H⁺

2 × Fe(III)-[cytochrome c] + succinate (Bound ligand (Het Group name = SIN) corresponds exactly) = fumarate + 2 × Fe(II)-[cytochrome c] + 2 × H(+)

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

Added reference

DOI no: 10.1038/70051

Nat Struct Biol 6:1113-1117 (1999)

PubMed id: 10581551

Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1.

D.Leys, A.S.Tsapin, K.H.Nealson, T.E.Meyer, M.A.Cusanovich, J.J.Van Beeumen.

ABSTRACT

Fumarate respiration is one of the most widespread types of anaerobic respiration. The soluble fumarate reductase of Shewanella putrefaciens MR-1 is a periplasmic tetraheme flavocytochrome c. The crystal structures of the enzyme were solved to 2.9 A for the uncomplexed form and to 2.8 A and 2.5 A for the fumarate and the succinate-bound protein, respectively. The structures reveal a flexible capping domain linked to the FAD-binding domain. A catalytic mechanism for fumarate reduction based on the structure of the complexed protein is proposed. The mechanism for the reverse reaction is a model for the homologous succinate dehydrogenase (complex II) of the respiratory chain. In flavocytochrome c fumarate reductase, all redox centers are in van der Waals contact with one another, thus providing an efficient conduit of electrons from the hemes via the FAD to fumarate.

Selected figure(s)

Figure 1.
Figure 1. Protein fold of the soluble fumarate reductase. a,b, Ribbon representation of fumarate reductase; molecule A of the orthorhombic crystal form is depicted. The cytochrome domain I is in orange and domains II, III and IV are in light blue, dark blue and green, respectively. The orientation in (b) is rotated 90° counter-clockwise horizontally and 90° clockwise along the vertical axis with respect to (a). Both figures were made using Molscript^30 and Raster3D^31. c, Superposition of the structures of fumarate reductase in the tetragonal form (green) and the orthorhombic crystal (molecule A, red; molecule D, blue) using the C coordinates of the FAD binding domain as the reference (figure generated using TURBO-FRODO^28). The view is approximately along the axis of rotation around the double hinge (see text) situated near residue 503. For clarity, only domains I, II and IV in molecule D of the orthorhombic crystal form (black lines) are shown.

Figure 3.
Figure 3. Stereo representation of the redox centers in fumarate reductase. Hemes are colored yellow (except the iron atoms, which are orange), FAD blue and the substrate green. The figure was prepared using Molscript^30 and Raster3D^31.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 1113-1117) copyright 1999.

Figures were selected by an automated process.