Structures and Solution Properties of Two Novel Periplasmic Sensor Domains with c-Type Heme from Chemotaxis Proteins of Geobacter sulfurreducens: Implications for Signal Transduction

Pokkuluri, P.R.; Pessanha, Miguel; Londer, Yuri Y.; Wood, Stephen; Duke, N.E.C.; Wilton, Rosemarie; Catarino, Teresa; Salgueiro, Carlos A.; Schiffer, M.

doi:10.1016/j.jmb.2008.01.087

Cited by 52 publications

(102 citation statements)

References 54 publications

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“…This is supported, not only by our current analysis, but also by an increasing number of such structures, part of SK proteins from various organisms, available in the PDB (e.g., see references 24, 25, 27, and 34). Some recent publications and new structures deposited into the PDB demonstrate that extracytoplasmic PAS-like domains are not confined to SK proteins but are also part of Mcp proteins we studied previously (26), other Mcp proteins (PDB codes 3c38 and 2qhk), and a GGDEF signaling protein (PDB code 2p7j). Homology modeling has revealed two tandem PAS domains for the extracytoplasmic sensing domain of B. subtilis asparagine chemotaxis receptor McpB (9).…”

Section: Vol 192 2010 Notes 1157mentioning

confidence: 81%

“…Of the 35 SKs, five were found to be soluble, whereas 30 contained at least one identifiable transmembrane helix. In the original work, the extracytoplasmic portions of the transmembrane histidine kinases did not receive any further attention.We recently determined the structures of two periplasmic sensor domains of chemotaxis receptor proteins (Mcp's) from the Gram-negative bacterium Geobacter sulfurreducens (26) and found that they adopted a PAS-like fold, as we had previously predicted (20), by using the structure prediction program 3DPSSM (17). This program combines one-and threedimensional amino acid sequence profiles with secondary structure predictions and solvation potential.…”

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confidence: 99%

“…We recently determined the structures of two periplasmic sensor domains of chemotaxis receptor proteins (Mcp's) from the Gram-negative bacterium Geobacter sulfurreducens (26) and found that they adopted a PAS-like fold, as we had previously predicted (20), by using the structure prediction program 3DPSSM (17). This program combines one-and threedimensional amino acid sequence profiles with secondary structure predictions and solvation potential.…”

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confidence: 99%

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Extracytoplasmic PAS-Like Domains Are Common in Signal Transduction Proteins

Chang

Tesar

et al. 2010

J Bacteriol

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We present the crystal structure of the extracytoplasmic domain of the Bacillus subtilis PhoR sensor histidine kinase, part of a two-component system involved in adaptation to low environmental phosphate concentrations. In addition to the PhoR structure, we predict that the majority of the extracytoplasmic domains of B. subtilis sensor kinases will adopt a fold similar to the ubiquitous PAS domain.Transmembrane signal transduction in bacteria is primarily mediated by the so-called two-component signal transduction system. To generate an appropriate response to an environmental signal, a sensor histidine kinase (SK) adjusts its intrinsic autokinase activity upon detection of ligands. Subsequent transfer of the phosphoryl group alters the propensity of the associated response regulator/transcription factor (RR) to generate the appropriate response (11).SK proteins are modular multidomain proteins featuring a structurally conserved C-terminal catalytic core and N-terminal signal-sensing and activity-modulating domains (31). The C-terminal catalytic core consists of two domains, the phosphorylatable histidine containing a four-helix bundle domain (called DHp or HisKA domain) and an ATP-binding domain (called HATPase or CA domain). The autokinase activity of the catalytic core is controlled by the N terminus, which is variable in length and domain architecture. Since the majority of SKs are transmembrane proteins, they commonly feature signal detection and activity-modulating domains localized to both the extracytoplasmic space and the cytoplasm.The cytoplasmic input and activity-modulating domains of the SKs are readily identifiable by sequence analysis, and the dominant folds are the HAMP, GAF, and PAS domains (reviewed in reference 31). The PAS fold is a particularly widespread and versatile protein domain fold, is commonly found in signaling proteins, and has been implicated in small-molecule binding as well as protein-protein interaction (21, 32). The Pfam database (7) reveals over 20,000 examples in more than 1,300 organisms.The extracytoplasmic domains in contrast to cytoplasmic portions of transmembrane-embedded SKs show very low sequence conservation. With a few exceptions, the extracytoplasmic sensing domains cannot be categorized by sequence analysis (11,31,35). This hampers progress in the identification of signaling ligands, which for most SKs still remain unknown.Here, we present a structure prediction analysis of the complete set of extracytoplasmic sensor domains of the Bacillus subtilis SK proteins. This analysis suggests that the PAS-like fold (10, 21) is the dominant sensing module adopted in B. subtilis SKs. To back up this prediction, we present the crystal structure of the B. subtilis PhoR extracytoplasmic domain, which adopts the expected PAS-like fold.B. subtilis two-component systems have been the subject of extensive studies in the last 3 decades. Some of these studies have identified growth conditions under which individual systems are activated (e.g., cell envelope stress, phosphate limita...

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Section: Vol 192 2010 Notes 1157mentioning

confidence: 81%

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confidence: 99%

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confidence: 99%

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Extracytoplasmic PAS-Like Domains Are Common in Signal Transduction Proteins

Chang

Tesar

et al. 2010

J Bacteriol

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“…6C) are somewhat different from those of AHR and CLOCK:BMAL1. In addition, some prokaryotic proteins with only one PAS domain also use both ␤-sheets and terminal ␣-helices to form diverse dimer interfaces, such as those seen with the sensor histidine kinase FixL (40) from Sinorhizobium meliloti, the signal transduction histidine kinase STHK (41) from Nostoc punctiforme, and the methyl-accepting chemotaxis protein GSU0935 (42) from Geobacter sulfurreducens (Fig. 6A).…”

Section: Discussionmentioning

confidence: 99%

Structure and Dimerization Properties of the Aryl Hydrocarbon Receptor PAS-A Domain

Potluri

Kim

et al. 2013

Molecular and Cellular Biology

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The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that binds to xenobiotics and responds by regulating the expression of gene programs required for detoxification and metabolism. AHR and its heterodimerization partner aryl hydrocarbon receptor nuclear translocator (ARNT) belong to the basic helix-loop-helix (bHLH)-PER-ARNT-SIM (PAS) family of transcription factors. Here we report the 2.55-Å-resolution crystal structure of the mouse AHR PAS-A domain, which represents the first AHR-derived protein structure. The AHR PAS-A domain forms a helix-swapped homodimer in the crystal and also in solution. Through a detailed mutational analysis of all interface residues, we identified several hydrophobic residues that are important for AHR dimerization and function. Our crystallographic visualization of AHR PAS-A dimerization leads us to propose a mode of heterodimerization with ARNT that is supported by both biochemical and cell-based data. Our studies also highlight the residues of other mammalian bHLH-PAS proteins that are likely involved in their homo-or heterodimerization.

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“…However, only a few of them have been purified and characterized. They include PpcA, an abundant triheme periplasmic c-type cytochrome that plays an important role in Fe(III) reduction (28,38,43), as well as several monoheme cytochromes that may play a sensory role (22,44,45). None of the outer-surface c-type cytochromes has been purified to homogeneity.…”

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confidence: 99%

Purification and Characterization of OmcZ, an Outer-Surface, Octaheme c -Type Cytochrome Essential for Optimal Current Production by Geobacter sulfurreducens

Inoue

Qian

Morgado

et al. 2010

Appl Environ Microbiol

242

185

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Previous studies have demonstrated that Geobacter sulfurreducens requires the c-type cytochrome OmcZ, which is present in large (OmcZ L ; 50-kDa) and small (OmcZ S ; 30-kDa) forms, for optimal current production in microbial fuel cells. This protein was further characterized to aid in understanding its role in current production. Subcellular-localization studies suggested that OmcZ S was the predominant extracellular form of OmcZ. N-and C-terminal amino acid sequence analysis of purified OmcZ S and molecular weight measurements indicated that OmcZ S is a cleaved product of OmcZ L retaining all 8 hemes, including 1 heme with the unusual c-type heme-binding motif CX 14 CH. The purified OmcZ S was remarkably thermally stable (thermaldenaturing temperature, 94.2°C). Redox titration analysis revealed that the midpoint reduction potential of OmcZ S is approximately ؊220 mV (versus the standard hydrogen electrode [SHE]) with nonequivalent heme groups that cover a large reduction potential range (؊420 to ؊60 mV). OmcZ S transferred electrons in vitro to a diversity of potential extracellular electron acceptors, such as Fe(III) citrate, U(VI), Cr(VI), Au(III), Mn(IV) oxide, and the humic substance analogue anthraquinone-2,6-disulfonate, but not Fe(III) oxide. The biochemical properties and extracellular localization of OmcZ suggest that it is well suited for promoting electron transfer in current-producing biofilms of G. sulfurreducens.

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Structures and Solution Properties of Two Novel Periplasmic Sensor Domains with c-Type Heme from Chemotaxis Proteins of Geobacter sulfurreducens: Implications for Signal Transduction

Cited by 52 publications

References 54 publications

Extracytoplasmic PAS-Like Domains Are Common in Signal Transduction Proteins

Extracytoplasmic PAS-Like Domains Are Common in Signal Transduction Proteins

Structure and Dimerization Properties of the Aryl Hydrocarbon Receptor PAS-A Domain

Purification and Characterization of OmcZ, an Outer-Surface, Octaheme c -Type Cytochrome Essential for Optimal Current Production by Geobacter sulfurreducens

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