PDBsum entry 1krh

Oxidoreductase

PDB id: 1krh

Contents

Protein chains

337 a.a. *

Ligands

SO4 ×5

FES ×2

FAD ×2

Waters ×364

* Residue conservation analysis

PDB id:

1krh

Name:

Oxidoreductase

Title:

X-ray structure of benzoate dioxygenase reductase

Structure:

Benzoate 1,2-dioxygenase reductase. Chain: a, b. Engineered: yes

Source:

Acinetobacter sp.. Organism_taxid: 472. Gene: benc. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.50Å R-factor: 0.242 R-free: 0.249

Authors:

A.Karlsson,Z.M.Beharry,D.M.Eby,E.D.Coulter,E.L.Niedle,D.M.Kurtz Jr., H.Eklund,S.Ramaswamy

Key ref:

A.Karlsson et al. (2002). X-ray crystal structure of benzoate 1,2-dioxygenase reductase from Acinetobacter sp. strain ADP1. J Mol Biol, 318, 261-272. PubMed id: 12051836 DOI: 10.1016/S0022-2836(02)00039-6

Date:

09-Jan-02 Release date: 15-May-02

Protein chains

P07771  (BENC_ACIAD) -  Benzoate 1,2-dioxygenase electron transfer component from Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

Seq: 348 a.a.

Struc: 337 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.1.18.1.3 - ferredoxin--NAD(+) reductase.
• Reaction:
  1. 2 reduced [2Fe-2S]-[ferredoxin] + NAD⁺ + H⁺ = 2 oxidized [2Fe- 2S]-[ferredoxin] + NADH
  2. reduced 2[4Fe-4S]-[ferredoxin] + NAD⁺ + H⁺ = oxidized 2[4Fe-4S]- [ferredoxin] + NADH
• 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: 10.1016/S0022-2836(02)00039-6

J Mol Biol 318:261-272 (2002)

PubMed id: 12051836

X-ray crystal structure of benzoate 1,2-dioxygenase reductase from Acinetobacter sp. strain ADP1.

A.Karlsson, Z.M.Beharry, D.Matthew Eby, E.D.Coulter, E.L.Neidle, D.M.Kurtz, H.Eklund, S.Ramaswamy.

ABSTRACT

One of the major processes for aerobic biodegradation of aromatic compounds is initiated by Rieske dioxygenases. Benzoate dioxygenase contains a reductase component, BenC, that is responsible for the two-electron transfer from NADH via FAD and an iron-sulfur cluster to the terminal oxygenase component. Here, we present the structure of BenC from Acinetobacter sp. strain ADP1 at 1.5 A resolution. BenC contains three domains, each binding a redox cofactor: iron-sulfur, FAD and NADH, respectively. The [2Fe-2S] domain is similar to that of plant ferredoxins, and the FAD and NADH domains are similar to members of the ferredoxin:NADPH reductase superfamily. In phthalate dioxygenase reductase, the only other Rieske dioxygenase reductase for which a crystal structure is available, the ferredoxin-like and flavin binding domains are sequentially reversed compared to BenC. The BenC structure shows significant differences in the location of the ferredoxin domain relative to the other domains, compared to phthalate dioxygenase reductase and other known systems containing these three domains. In BenC, the ferredoxin domain interacts with both the flavin and NAD(P)H domains. The iron-sulfur center and the flavin are about 9 A apart, which allows a fast electron transfer. The BenC structure is the first determined for a reductase from the class IB Rieske dioxygenases, whose reductases transfer electrons directly to their oxygenase components. Based on sequence similarities, a very similar structure was modeled for the class III naphthalene dioxygenase reductase, which transfers electrons to an intermediary ferredoxin, rather than the oxygenase component.

Selected figure(s)

Figure 3.
Figure 3. Stereo representation of the [2Fe-2S] center in BenC. The center is connected to the protein via cysteine residues 41, 46, 49 and 83, which ligate the two iron atoms as well as by an intricate hydrogen bonding pattern, represented by broken red lines, to the cysteine sulfur atoms and bridging sulfides.

Figure 4.
Figure 4. FAD binding in BenC. (a) The FAD-binding site is situated between the FAD-binding domain, in yellow, and the NADH-binding domain, in blue. The methyl groups of the isoalloxazine ring are pointing towards the [2Fe-2S] center in the ferredoxin-like domain. The FAD is represented inside a F[o] -F[c] map, colored in green, contoured at 4×rms. The picture was made with the program BOBSCRIPT (http://www.strubi.ox.ac.uk/bobscript/). (b) A close-up of the FAD molecule binding to the NADH and FAD binding domains of BenC. There are five water molecules contributing to the extensive hydrogen bonding holding the FAD in position. The stacking interaction between Phe335 and the isoalloxazine ring of the FAD can be seen at the bottom right of the Figure.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 261-272) copyright 2002.

Figures were selected by the author.