The Q-linker: a class of interdomain sequences found in bacterial multidomain regulatory proteins

Wootton, John C.; Drummond, Martin

doi:10.1093/protein/2.7.535

Cited by 199 publications

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“…The C-terminal domain contains a winged helix-turn-helix motif that binds DNA (33)(34)(35). The two domains are connected to one another via an exposed Q linker (36) that is sensitive to proteolysis (37). In this study, we report that DNA binding in the C-terminal region of OmpR stimulates phosphorylation at the N terminus.…”

mentioning

confidence: 73%

C-terminal DNA binding stimulates N-terminal phosphorylation of the outer membrane protein regulator OmpR from Escherichia coli

Ames

Frankema

Kenney

1999

Proc. Natl. Acad. Sci. U.S.A.

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Expression of the porin genes of Escherichia coli is regulated in part by the osmolarity of the growth medium. The process is controlled by the histidine kinase EnvZ and the response regulator OmpR. We have previously shown that phosphorylation of OmpR increases its affinity for the upstream regulatory regions of ompF and ompC. We now report that, in the presence of DNA, there is a dramatic stimulation in the level of phospho-OmpR. This effect is independent of the source of phosphorylation, i.e., stimulation of phosphorylation is observed with a small phosphorylating agent such as acetyl phosphate or with protein-catalyzed phosphorylation by the kinase EnvZ. The dephosphorylation rate of phospho-OmpR is affected only slightly by the presence of DNA; thus, the increased level is largely caused by an increased rate of phosphorylation. Stimulation of phosphorylation requires specific binding of DNA by OmpR. Occupancy of the DNA binding domain exposes a trypsin cleavage site in the linker, which connects the phosphorylation domain with the DNA binding domain. Our results indicate that when DNA binds in the C terminus, it enhances phosphorylation in the N terminus, and the linker undergoes a conformational change. A generalized mechanism involving a four-state model for response regulators is proposed.winged helix-turn-helix ͉ response regulator ͉ porin regulation ͉ two-component regulatory system ͉ transcriptional activator A ll organisms must communicate with their environment to survive. Two-component regulatory systems have emerged as a paradigm for adaptive responses. In its simplest form, a two-component system contains a sensor, a histidine kinase, and a response regulator, often a transcriptional activator. Changes in the environment result in phosphorylation of the sensor followed by transphosphorylation onto the response regulator. Adaptive responses controlled by two-component regulatory systems are diverse and include chemotaxis, fruit ripening, sporulation, and virulence gene expression in numerous pathogens (see ref. 1).The outer membrane proteins OmpF and OmpC in Escherichia coli are regulated in response to changes in the osmolarity of the medium (see ref. 2 for a recent review). At low osmolarity, OmpF predominates; at high osmolarity, ompF is repressed, and OmpC is the major porin in the outer membrane (3). This process is controlled by the EnvZ͞OmpR two-component regulatory system (4). EnvZ is a histidine kinase located in the inner membrane, OmpR is a cytoplasmic DNA binding protein (5). The two proteins communicate via a series of phosphorylation and phosphotransfer reactions. EnvZ senses the osmotic environment and is autophosphorylated from intracellular ATP at His-243 (6, 7). EnvZ-P phosphorylates OmpR at , and phospho-OmpR (OmpR-P) binds to the upstream sites of the porin genes to regulate their expression (9-12). EnvZ also stimulates the dephosphorylation of OmpR-P, thereby controlling the concentration of cellular OmpR-P (11, 13). Phosphorylation of OmpR results in an increase in its affin...

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mentioning

confidence: 73%

C-terminal DNA binding stimulates N-terminal phosphorylation of the outer membrane protein regulator OmpR from Escherichia coli

Ames

Frankema

Kenney

1999

Proc. Natl. Acad. Sci. U.S.A.

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“…9 Lys, 1 Arg, 6 Glu), but also contains 4 Pro. This sequence does not resemble any of the other well characterised linker regions in proteins; such as the 'Q' linkers located at the boundaries of domains in bacterial regulatory and sensory transduction proteins [28], the linkers characterised by Ala-Pro repeats which are common in decarboxylases and dehydrogenases [29] or the 'LKTPGRED' linkers from bacterial phosphotransferase system enzymes [30]. However, it does contain a preponderance of amino acids considered favourable as constituents of inter-domain linkers [31].…”

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confidence: 89%

Structural and enzymological analysis of the interaction of isolated domains of cytochrome P‐450 BM3

et al. 1994

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Structural and enzymological analysis of the interaction of isolated domains of cytochrome P-450 BM3 AhstractThe interactions of the individually expressed haem-and flavin-containing domains of cytochrome P-450 BM3 have been analysed by enzymological and spectroscopic techniques. Electron transfer between the isolated domains occurs at a much lower rate than that occurring in the intact flavocytochrome. CD spectroscopic studies indicate that the linkage of the domains in intact P-450 BM3 creates haem and amino acid environments suitable for efficient electron transfer from its flavin domain.Key w&r: ~t~~ro~~ P-450 BM3; Domain inter~t~o~~ Circular dichroism; Electron transfer; Raem environmentThe cytochrome P-450 BM3 system from Bacillus megaterium provides a unique bacterial model for mammalian P-450 systems, such as those involved in drug and xenobiotic metabolism [l-3]. It is the only characterised prokaryotic class II P-450 utilising an FADIFMN containing NADPH-P-450 reductase as an electron transfer partner [4]. Other prokaryotic (class I) systems operate a three protein-~om~nent electron transfer chain with electrons flowing from NAD(P)H onto an FADcontaining redoxin reductase, through an iron-sulphur redoxin and onto the P-450 (e.g. [5]). In addition, P-450 BM3 has its redox partners fused in a single polypeptide chain, with the haem-containing P-450 'domain' being N-terminal and the flavincontaining reductase C-terminal [4,6]. The only structurally analogous P-450 yet characterised is the cell signalling enzyme nitric oxide (NO) synthase [71-Like all proka~oti& P-45&, P-450 BM3 is a soluble enzyme. This has enabled relatively simple p~~~a~on of the ~l~p~de [4]. The gene has been cloned and expressed in E, co& [S,9], as have the sub-genes encoding *Corresponding author. Fax: (44) (41) 330 4620.

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“…The signal peptide is followed by a stretch of about 50 amino acids of unknown function. Next comes a roughly 30-residue proline/serine/glutamine-rich segment, absent in HhoA and HhoB, which has the characteristics of a Q-linker (a flexible segment linking domains) (M. J. Pallen, unpublished; Wootton and Drummond, 1989).…”

Section: Amino Acid Sequencementioning

confidence: 99%

The HtrA family of serine proteases

Pallen¹,

Wren²

1997

Molecular Microbiology

367

408

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SummaryHtrA, also known as DegP and probably identical to the Do protease, is a heat shock-induced serine protease that is active in the periplasm of Escherichia coli. Homologues of HtrA have been described in a wide range of bacteria and in eukaryotes. Its chief role is to degrade misfolded proteins in the periplasm. Substrate recognition probably involves the recently described PDZ domains in the C-terminal half of HtrA and, we suspect, has much in common with the substrate recognition system of the tail-specific protease, Prc (which also possesses a PDZ domain). The expression of htrA is regulated by a complex set of signal transduction pathways, which includes an alternative sigma factor, RpoE, an anti-sigma factor, RseA, a two-component regulatory system, CpxRA, and two phosphoprotein phosphatases, PrpA and PrpB. Mutations in the htrA genes of Salmonella, Brucella and Yersinia cause decreased survival in mice and/or macrophages, and htrA mutants can act as vaccines, as cloning hosts and as carriers of heterologous antigens.

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The Q-linker: a class of interdomain sequences found in bacterial multidomain regulatory proteins

Cited by 199 publications

References 0 publications

C-terminal DNA binding stimulates N-terminal phosphorylation of the outer membrane protein regulator OmpR from Escherichia coli

C-terminal DNA binding stimulates N-terminal phosphorylation of the outer membrane protein regulator OmpR from Escherichia coli

Structural and enzymological analysis of the interaction of isolated domains of cytochrome P‐450 BM3

The HtrA family of serine proteases

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