Defining a direction: electron transfer and catalysis in Escherichia coli complex II enzymes

Abstract

There are two homologous membrane-bound enzymes in Escherichia coli that catalyze reversible conversion between succinate/fumarate and quinone/quinol. Succinate:ubiquinone reductase (SQR) is a component of aerobic respiratory chains, whereas quinol:fumarate reductase (QFR) utilizes menaquinol to reduce fumarate in a final step of anaerobic respiration. Although, both protein complexes are capable of supporting bacterial growth on either minimal succinate or fumarate media, the enzymes are more proficient in their physiological directions. Here we evaluate factors that may underlie this catalytic bias. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.

Figure 1. E. coli SQR and QFR

(A) Catalytic activity (TN, turnover number) of SQR and QFR with UQ and MQ [43]. (B) The overall structures and spatial arrangement redox centers in E. coli QFR (pdb: 1KF6 [7], left) and SQR (pdb:2WDQ [39], right). The flavoprotein subunits (SdhA/FrdA) are shown in blue; the iron protein subunits (SdhB/FrdB) are in purple. The transmembrane subunits are in pink (SdhC/FrdC) and gray (SdhD/FrdD). The specific quinone site inhibitor 2-n-heptyl-4-hydroxyquinoline-N-oxide (HQNO) for QFR is shown in cyan and the specific quinone site inhibitor carboxin for SQR is shown in green. Oxaloacetate bound near the isoalloxazine ring of FAD is shown in magenta. The edge-to-edge distances (Å) of redox active centers are indicated. The partial reactions at the catalytic sites are diagrammed in the QFR structure.

Figure 2. Electron transfer pathways between FAD and [2Fe-2S] cluster

(A) The structure of W. succinogenes QFR (pdb: 2BS2 [19]) demonstrates a water molecule hydrogen-bonded to His A45 and within van der Waals distance to Cys B55 [8]. This water mediates ET coupling pathway between FAD and the [2Fe-2S] cluster. (B) GREENPATH calculations outline the ET path in E. coli QFR (pdb:1KF6 [7]) according to [20]. Path 1 is calculated for the wild type structure and path 2 when Ala A47 was in silico mutated to Gly. SdhA/FrdA subunits and their residues are in blue and SdhB/FrdB in teal; the distances between the atoms (Å) are indicated next to the dashed lines.

Figure 3

Electron transfer pathways between iron-sulfur clusters in SdhB of E. coli SQR. The N-terminal [2Fe-2S] domain is shown in teal and C-terminal in purple. Dashed lines show through-space jumps. Path 1 (C75, A74, L73, and 3.8 Å jump to C152) and Path 2 (C60, G61, and 3.8 Å jump to C152) are for [2Fe-2S] and [4Fe-4S] centers. Path 3 (C155 and 3.8 Å jump to C152) is for [4Fe-4S] and [3Fe-4S]. Residues involved in ET are shown as sticks, while other ligating residues are shown as thin lines.

Figure 4. Spatial arrangements of redox groups in the hydrophobic domain and [3Fe-4S] cluster in E. coli complex II enzymes

(A) In QFR Cys B204 and Thr B205 mediate electron transfer between MQ and [3Fe-4S]. (B) His B207 in SQR provides ET coupling between [3Fe-4S] and heme b. Ile B209 is a residue mediating ET between UQ and [3Fe-4S]. Carboxin occupies a position deep in the UQ binding site and within van der Waals distance to the heme propionate. This would be similar to the position of UQ during catalysis and within effective ET distance to heme b.

Figure 5. Role of the hydrophilic substitutions in quinone rings for SQR catalytic activity

(A) Ubiquinone at the active site of avian SQR (pdb:1YQ3 [37]). (B) Chemical structures of quinones substrates for SQR. (C) Catalytic activity of E. coli SQR in succinate-oxidase and fumarate-reductase reactions with different quinones [30, 43].