Breaking the Carboxyl Rule

Abstract

Background: Lysine rather than a carboxylic residue is in place of the internal proton donor in the E. sibiricum proton pump. Results: H ϩ uptake precedes reprotonation of the retinal Schiff base. K96A mutation slows it by Ͼ100-fold.

A new group of eubacterial light-driven retinal-binding proton pumps with an unusual cytoplasmic proton donor

“…formation of BR are often associated with proton transfers in hydrogen-bonded networks [90,91]. While the KIE observed for the overall M rise of PspR (~4.5) is similar to that observed for BR (~5), the KIE for the overall M decay (~3.5) is larger than in BR (~1.8) [91], and similar to the one observed for ESR [41]. This is consistent with a mechanism of Schiff base reprotonation different from the classical BR-like mechanism with a carboxylic proton donor, and possibly involving hydrogen-bonded networks, in line with the polar nature of the cytoplasmic half of PspR.…”

“…Roughly, the tree can be broken into the two main branches, with the lower branch being dominated by PR-like and XR-like proton pumps (the latter includes actinorhodopsins) as well as chloride and sodium pumps (so-called NTQ and NDQ types). This branch also includes the unique protonpumping rhodopsins from Exiguobacterium (ESR) mentioned above, in which the carboxylic donor is replaced by Lys [41,42]. The upper branch, which is more closely related to archaeal rhodopsins (represented by BR-like proton pumps) contains ASR-like photosensors (also known as xenorhodopsins) [58] and another unknown group, tagged with three question marks in Figure 1.…”

“…Second, more striking departure from "the carboxyl rule" [41] is that found in Exiguobacterium, where the carboxylic proton donor is replaced by Lys [42]. Unlike the typical carboxylic proton donors, this lysine residue resides in a hydrophilic cavity and may form a proton-donating complex with water molecules [41,43].…”

“…The consensus on the general mechanism emerging from these studies looks fairly simple and involves only three important elements: the retinal Schiff base with lysine sidechain on helix G (Lys216 in BR), primary proton acceptor on the extracellular side of helix C (Asp85 in BR, usually in complex with His in PR and XR) [28][29][30], and proton donor (usually carboxylic, Asp96 in BR) on the cytoplasmic side of helix C. Upon photoisomerization of the retinal chromophore of the light-adapted parent state (from all-trans-to 13-cis-), the Schiff base proton is transferred to the primary proton acceptor, and this transfer is normally mediated by a strongly hydrogen-bonded water molecule [31][32][33]. For the majority of proton-pumping rhodopsins, the second half of the photocycle involves the reprotonation of the Schiff base nitrogen from the cytoplasmic carboxylic proton donor, which does not interact with the Schiff base directly, but rather communicates with it via a number of water molecules entering the cytoplasmic half of the protein after a conformational change [34,35].…”

Molecular details of the unique mechanism of chloride transport by a cyanobacterial rhodopsin

“…12,[15][16][17] According to this classification, most archaeal and fungal proton pumps have DTD motifs, while bacterial proton pumps (proteorhodopsins and xanthorhodopsins) most commonly display DTE, even though some cases of DTK and DTG proton pumps have been identified. 18,19 In contrast, lightdriven sodium pumps have NDQ motifs, in which the primary proton acceptor of the Schiff base shifts to the second position. 20 Compared to light-driven cation transport, anion transport by microbial rhodopsins has not been studied as extensively.…”