Thermoplasma
Mycoplasmatales
Thermoplasmales
Glyceryl Ethers
Glucose Dehydrogenases
Multienzyme Complexes
Allosteric control of three B12-dependent (class II) ribonucleotide reductases. Implications for the evolution of ribonucleotide reduction. (1/178)
Three separate classes of ribonucleotide reductases are known, each with a distinct protein structure. One common feature of all enzymes is that a single protein generates each of the four deoxyribonucleotides. Class I and III enzymes contain an allosteric substrate specificity site capable of binding effectors (ATP or various deoxyribonucleoside triphosphates) that direct enzyme specificity. Some (but not all) enzymes contain a second allosteric site that binds only ATP or dATP. Binding of dATP to this site inhibits the activity of these enzymes. X-ray crystallography has localized the two sites within the structure of the Escherichia coli class I enzyme and identified effector-binding amino acids. Here, we have studied the regulation of three class II enzymes, one from the archaebacterium Thermoplasma acidophilum and two from eubacteria (Lactobacillus leichmannii and Thermotoga maritima). Each enzyme has an allosteric site that binds ATP or various deoxyribonucleoside triphosphates and that regulates its substrate specificity according to the same rules as for class I and III enzymes. dATP does not inhibit enzyme activity, suggesting the absence of a second active allosteric site. For the L. leichmannii and T. maritima enzymes, binding experiments also indicate the presence of only one allosteric site. Their primary sequences suggest that these enzymes lack the structural requirements for a second site. In contrast, the T. acidophilum enzyme binds dATP at two separate sites, and its sequence contains putative effector-binding amino acids for a second site. The presence of a second site without apparent physiological function leads to the hypothesis that a functional site was present early during the evolution of ribonucleotide reductases, but that its function was lost from the T. acidophilum enzyme. The other two B12 enzymes lost not only the function, but also the structural basis for the site. Also a large subgroup (Ib) of class I enzymes, but none of the investigated class III enzymes, has lost this site. This is further indirect evidence that class II and I enzymes may have arisen by divergent evolution from class III enzymes. (+info)Structure of VAT, a CDC48/p97 ATPase homologue from the archaeon Thermoplasma acidophilum as studied by electron tomography. (2/178)
Valosine-containing protein-like ATPase from Thermoplasma acidophilum is a member of the superfamily of ATPases associated with a diversity of cellular activities and is closely related to CDC48 from yeast and p97 from higher eukaryotes and more distantly to N-ethylmaleimide-sensitive fusion protein. We have used electron tomography to obtain low-resolution (2-2.5 nm) three-dimensional maps of both the whole 500 kDa complex and the N-terminally truncated valosine-containing protein-like ATPase from T. acidophilum complex lacking the putative substrate binding domain. (+info)Isolation and characterization of novel neutral glycolipids from Thermoplasma acidophilum. (3/178)
Several novel neutral glycolipids (GL-1a, GL-1b, GL-2a, GL-2b and GL-2c) were isolated from Thermoplasma acidophilum by high-performance liquid chromatography using phenylboronic acid-silica and preparative thin-layer chromatography. The tentative structures of these lipids were characterized by the combination of gas-liquid chromatography, the methylation procedure, and (1)H-NMR and FAB-mass spectrometries. The lipophilic portion of the neutral glycolipids was composed of a simple molecular species named caldarchaeol (dibiphytanyl-diglycerol tetraether). The sugar moieties of these glycolipids were composed of gulose and glucose which formed monosaccharide residues on one side or both sides of the core lipids. Gulose was attached to the terminal glycerol OH group of the core lipid with a beta-configuration and glucose being attached with an alpha-configuration. The proposed structure of GL-1a was gulosylcaldarchaeol and that of GL-1b was glucosylcaldarchaeol. The structures of GL-2a, GL-2b, and GL-2c were the analogs of the caldarchaeol derivatives attached by a variety of gulosyl residues or glucosyl residues on both sides of the terminal OH groups. (+info)Giant proteases: beyond the proteasome. (4/178)
Proteasomes and related proteases are thought to be the principal machinery responsible for intracellular protein degradation. A new class of giant proteases has been discovered that can augment the catabolic functions of proteasomes and, under some conditions, may even substitute for proteasomes altogether. (+info)The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element. (5/178)
BACKGROUND: The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. RESULTS: Using nuclear magnetic resonance (NMR) spectroscopy, we found that VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn (comprising residues Met1-Thr92) forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc (comprising residues Glu93-Gly185) forms a novel six-stranded beta-clam fold. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. Sequence and structure analyses showed that VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. These proteins map out an evolutionary path from simple homodimeric transcription factors containing a single copy of the VAT-Nn repeat to complex enzymes containing four copies. CONCLUSIONS: Our results suggest that VAT-N is a precursor of the aspartic proteinases that has acquired peptide-binding activity while remaining proteolytically incompetent. We propose that the binding site of the protein is similar to that of aspartic proteinases, in that it lies between the psi-loops of the amino-terminal beta-barrel and that it coincides with a crescent-shaped band of positive charge extending across the upper face of the molecule. (+info)Conformational rearrangements of an archaeal chaperonin upon ATPase cycling. (6/178)
Chaperonins are double-ring protein assemblies with a central cavity that provides a sequestered environment for in vivo protein folding. Their reaction cycle is thought to consist of a nucleotide-regulated alternation between an open substrate-acceptor state and a closed folding-active state. The cavity of ATP-charged group I chaperonins, typified by Escherichia coli GroEL [1], is sealed off by a co-chaperonin, whereas group II chaperonins--the archaeal thermosome and eukaryotic TRiC/CCT [2]--possess a built-in lid [3-5]. The mechanism of the lid's rearrangements requires clarification, as even in the absence of nucleotides, thermosomes of Thermoplama acidophilum appear open in vitrified ice [6] and closed in crystals [4]. Here we analyze the conformation of the thermosome at each step of the ATPase cycle by small-angle neutron scattering. The apo-chaperonin is open in solution, and ATP binding induces its further expansion. Closure seems to occur during ATP hydrolysis and before phosphate release, and represents the rate-limiting step of the cycle. The same closure can be triggered by the crystallization buffer. Thus, the allosteric regulation of group II chaperonins appears different from that of their group I counterparts. (+info)Glucosylcaldarchaetidylglycerol, a minor phosphoglycolipid from Thermoplasma acidophilum. (7/178)
A novel phosphoglycolipid (GPL-K) was isolated from Thermoplasma acidophilum (ATCC 27658). The chemical components of GPL-K were analyzed by gas liquid chromatography and GC-MS. The sugar moiety of GPL-K and its anomeric region were analyzed by NMR assignment. The core lipid of GPL-K was caldarchaeol, and its main hydrocarbon chains were acyclic and monocyclic C(40) biphytanyl. The polar head groups were alpha-glucose and glycerophosphate. The negative FAB-MS spectrum of GPL-K confirmed that the lipid peak of m/z 1614 consists of a caldarchaeol (including one cyclopentane ring), a hexose sugar, and a glycerophosphate. We have proposed the tentative structure of GPL-K. (+info)Why does threonine, and not serine, function as the active site nucleophile in proteasomes? (8/178)
Proteasomes belong to the N-terminal nucleophile group of amidases and function through a novel proteolytic mechanism, in which the hydroxyl group of the N-terminal threonines is the catalytic nucleophile. However, it is unclear why threonine has been conserved in all proteasomal active sites, because its replacement by a serine in proteasomes from the archaeon Thermoplasma acidophilum (T1S mutant) does not alter the rates of hydrolysis of Suc-LLVY-amc (Seemuller, E., Lupas, A., Stock, D., Lowe, J., Huber, R., and Baumeister, W. (1995) Science 268, 579-582) and other standard peptide amide substrates. However, we found that true peptide bonds in decapeptide libraries were cleaved by the T1S mutant 10-fold slower than by wild type (wt) proteasomes. In degrading proteins, the T1S proteasome was 3.5- to 6-fold slower than the wt, and this difference increased when proteolysis was stimulated using the proteasome-activating nucleotidase (PAN) ATPase complex. With mutant proteasomes, peptide bond cleavage appeared to be rate-limiting in protein breakdown, unlike with wt. Surprisingly, a peptide ester was hydrolyzed by both particles much faster than the corresponding amide, and the T1S mutant cleaved it faster than the wt. Moreover, the T1S mutant was inactivated by the ester inhibitor clasto-lactacystin-beta-lactone severalfold faster than the wt, but reacted with nonester irreversible inhibitors at similar rates. T1A and T1C mutants were completely inactive in all these assays. Thus, proteasomes lack additional active sites, and the N-terminal threonine evolved because it allows more efficient protein breakdown than serine. (+info)Thermoplasma is a genus of archaea, which are single-celled microorganisms that lack a nucleus and other membrane-bound organelles. Thermoplasma species are extremophiles, meaning they thrive in extreme environments that are hostile to most other life forms. Specifically, Thermoplasma species are thermoacidophiles, which means they grow optimally at relatively high temperatures (45-60°C) and low pH levels (around 2).
Thermoplasma species have an unusual way of dealing with the harsh conditions of their environment. They lack a cell wall, which makes them highly resistant to heat and acidity. Instead, they have a unique outer membrane that is composed of proteins and lipids, which provides stability and protection in extreme environments.
Thermoplasma species are found in various habitats, including self-heating coal refuse piles, sulfur-rich hot springs, and solfataric fields. They have also been isolated from the acidic environments of industrial waste sites and even from the human mouth. Thermoplasma species are important in biotechnology due to their ability to produce enzymes that can function under extreme conditions, making them useful for various industrial applications.
Archaeal proteins are proteins that are encoded by the genes found in archaea, a domain of single-celled microorganisms. These proteins are crucial for various cellular functions and structures in archaea, which are adapted to survive in extreme environments such as high temperatures, high salt concentrations, and low pH levels.
Archaeal proteins share similarities with both bacterial and eukaryotic proteins, but they also have unique features that distinguish them from each other. For example, many archaeal proteins contain unusual amino acids or modifications that are not commonly found in other organisms. Additionally, the three-dimensional structures of some archaeal proteins are distinct from their bacterial and eukaryotic counterparts.
Studying archaeal proteins is important for understanding the biology of these unique organisms and for gaining insights into the evolution of life on Earth. Furthermore, because some archaea can survive in extreme environments, their proteins may have properties that make them useful in industrial and medical applications.
Mycoplasmatales is an order of bacteria that lack a cell wall and are characterized by their small size and simple genome. They are commonly found in various environments, including the human body, where they can be part of the normal flora or associated with diseases. The order Mycoplasmatales contains several genera, including Mycoplasma, Ureaplasma, and Acholeplasma, among others. These bacteria can cause a variety of infections, such as respiratory tract infections, urinary tract infections, and sexually transmitted diseases. Due to their small size and lack of a cell wall, they can be resistant to many antibiotics, making them difficult to treat in some cases.
I'm sorry for any confusion, but "Thermoplasmales" is not a recognized term in medical or scientific nomenclature. It seems that there might be a spelling mistake or a misunderstanding of the correct term. If you meant to ask about Thermoplasmatales, which is an order of archaea (single-celled microorganisms), I would be happy to provide more information on that.
Thermoplasmatales are a group of extremophilic archaea, meaning they thrive in extreme environments that are hostile to most other life forms. They are typically found in environments with high temperatures (50-90°C), low pH levels (around 1-4), and high heavy metal concentrations. These organisms have unique adaptations that allow them to survive under such harsh conditions, including the ability to produce energy through sulfur metabolism and a unique cell wall structure that lacks peptidoglycan.
If you meant to ask about something else or need more information on Thermoplasmatales, please let me know!
Glyceryl ethers, also known as glycerol ethers or alkyl glycosides, are a class of compounds formed by the reaction between glycerol and alcohols. In the context of medical definitions, glyceryl ethers may refer to a group of naturally occurring compounds found in some organisms, including humans.
These compounds are characterized by an ether linkage between the glycerol molecule and one or more alkyl chains, which can vary in length. Glyceryl ethers have been identified as components of various biological tissues, such as lipid fractions of human blood and lung surfactant.
In some cases, glyceryl ethers may also be used as pharmaceutical excipients or drug delivery systems due to their unique physicochemical properties. For example, they can enhance the solubility and bioavailability of certain drugs, making them useful in formulation development. However, it is important to note that specific medical applications and uses of glyceryl ethers may vary depending on the particular compound and its properties.
Glucose dehydrogenases (GDHs) are a group of enzymes that catalyze the oxidation of glucose to generate gluconic acid or glucuronic acid. This reaction involves the transfer of electrons from glucose to an electron acceptor, most commonly nicotinamide adenine dinucleotide (NAD+) or phenazine methosulfate (PMS).
GDHs are widely distributed in nature and can be found in various organisms, including bacteria, fungi, plants, and animals. They play important roles in different biological processes, such as glucose metabolism, energy production, and detoxification of harmful substances. Based on their cofactor specificity, GDHs can be classified into two main types: NAD(P)-dependent GDHs and PQQ-dependent GDHs.
NAD(P)-dependent GDHs use NAD+ or NADP+ as a cofactor to oxidize glucose to glucono-1,5-lactone, which is then hydrolyzed to gluconic acid by an accompanying enzyme. These GDHs are involved in various metabolic pathways, such as the Entner-Doudoroff pathway and the oxidative pentose phosphate pathway.
PQQ-dependent GDHs, on the other hand, use pyrroloquinoline quinone (PQQ) as a cofactor to catalyze the oxidation of glucose to gluconic acid directly. These GDHs are typically found in bacteria and play a role in energy production and detoxification.
Overall, glucose dehydrogenases are essential enzymes that contribute to the maintenance of glucose homeostasis and energy balance in living organisms.
I'm happy to help! However, I believe there might be a slight mistake in your question. "Archaeal" is not a term used to describe genes but rather a group of single-celled organisms that are classified as archaea.
Archaea are one of the three domains of life, along with bacteria and eukaryotes (which include plants, animals, and fungi). Archaea are unique because they share characteristics with both bacteria and eukaryotes, but they also have many features that are distinctly their own. For example, archaea have a different cell membrane structure than bacteria and eukaryotes, which allows them to thrive in extreme environments such as hot springs, salt mines, and deep-sea vents.
Genes, on the other hand, are segments of DNA that contain the instructions for making proteins or performing other important functions in an organism's cells. All living organisms, including archaea, have genes that are passed down from generation to generation. Archaeal genes are made up of the same four nucleotides (A, T, C, and G) as bacterial and eukaryotic genes, and they code for proteins and RNA molecules that are essential for the survival and reproduction of archaea.
So, to summarize, there is no specific definition for "Archaeal genes" because "archaeal" is not a term used to describe genes. However, we can say that archaeal genes are segments of DNA that contain the instructions for making proteins and performing other important functions in archaea.
Multienzyme complexes are specialized protein structures that consist of multiple enzymes closely associated or bound together, often with other cofactors and regulatory subunits. These complexes facilitate the sequential transfer of substrates along a series of enzymatic reactions, also known as a metabolic pathway. By keeping the enzymes in close proximity, multienzyme complexes enhance reaction efficiency, improve substrate specificity, and maintain proper stoichiometry between different enzymes involved in the pathway. Examples of multienzyme complexes include the pyruvate dehydrogenase complex, the citrate synthase complex, and the fatty acid synthetase complex.
Methanobrevibacter is a genus of archaea (single-celled microorganisms) that are methanogens, meaning they produce methane as a metabolic byproduct. These organisms are commonly found in the digestive tracts of animals, including humans, where they help break down organic matter and recycle nutrients. They are strict anaerobes, requiring an environment free of oxygen to survive and grow. Some species within this genus have been associated with dental diseases such as periodontitis. However, more research is needed to fully understand their role in human health and disease.