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P-loop
The Walker A and Walker B motifs are protein sequence motifs, known to have highly conserved three-dimensional structures. These were first reported in ATP-binding proteins by Walker and co-workers in 1982.[1]Contents1 Walker A motif1.1 A-loop2 Walker B motif 3 See also 4 References 5 External linksWalker A motif[edit]Alignment of the H-Ras mutant A59G mutants in complex with GppNHp (green cartoon) and GDP (cyan cartoon). The P-loop main chain is shown in red, the Mg2+ ion as green sphere and the side chains of the amino acids K16 and S17 are shown as sticks.Walker A motif, also known as the Walker loop or P-loop (phosphate-binding loop) is a motif in proteins that is associated with phosphate binding. The motif has the pattern G-x(4)-GK-[TS], where G, K, T and S denote glycine, lysine, threonine and serine residues respectively, and x denotes any amino acid. It is present in many ATP or GTP utilizing proteins; it is the β phosphate of the nucleotide that is bound
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Sequence Motif
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance
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Aromatic Amino Acid
An aromatic amino acid (AAA)[1] is an amino acid that includes an aromatic ring. Examples include:Among 20 standard amino acids:Phenylalanine Tryptophan Tyrosine HistidineOthers:Thyroxine 5-Hydroxytryptophan L-DOPA Phenylalanine
Phenylalanine
Tyrosine
Tyrosine
L-DOPA
L-DOPA
→ (Dopamine) → (Epinephrine) → (Norepinephrine) Tryptophan
Tryptophan
→ 5-hydroxytryptophan → (Serotonin) Phenylalanine
Phenylalanine
Tyrosine
Tyrosine
→ Thyroxine Phenylalanine, tryptophan, and histidine are essential amino acids for animals. Since they are not synthesized in the human body, they must be derived from the diet. Tyrosine
Tyrosine
is semi-essential; it can be synthesized, but only from phenylalanine
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Protein Tyrosine Phosphatase
Protein tyrosine phosphatases are a group of enzymes that remove phosphate groups from phosphorylated tyrosine residues on proteins. Protein tyrosine (pTyr) phosphorylation is a common post-translational modification that can create novel recognition motifs for protein interactions and cellular localization, affect protein stability, and regulate enzyme activity. As a consequence, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions
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Pyridoxal Phosphate
Pyridoxal
Pyridoxal
phosphate (PLP, pyridoxal 5'-phosphate, P5P), the active form of vitamin B6, is a coenzyme in a variety of enzymatic reactions. The Enzyme commission has catalogued more than 140 PLP-dependent activities, corresponding to ~4% of all classified activities.[3] The versatility of PLP arises from its ability to covalently bind the substrate, and then to act as an electrophilic catalyst, thereby stabilizing different ty
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Cysteine Synthase
In enzymology, a cysteine synthase (EC 2.5.1.47) is an enzyme that catalyzes the chemical reaction O3-acetyl-L-serine
O3-acetyl-L-serine
+ hydrogen sulfide ⇌ displaystyle rightleftharpoons L-cysteine
L-cysteine
+ acetateThus, the two substrates of this enzyme are O3-acetyl-L-serine
O3-acetyl-L-serine
and hydrogen sulfide, whereas its two products are L-cysteine
L-cysteine
and acetate. This enzyme belongs to the family of transferases, specifically those transferring aryl or alkyl groups other than methyl groups
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Conformational Change
In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors. A macromolecule is usually flexible and dynamic. It can change its shape in response to changes in its environment or other factors; each possible shape is called a conformation, and a transition between them is called a conformational change. Factors that may induce such changes include:temperature, pH, voltage, ion concentration, phosphorylation, or the binding of a ligand.Laboratory analysis[edit] Many biophysical techniques such as crystallography, NMR, electron paramagnetic resonance (EPR) using spin label techniques, circular dichroism (CD), hydrogen exchange, and FRET can be used to study macromolecular conformational change
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Induced Fit Model
Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate chemical reactions. The molecules upon which enzymes may act are called substrates and the enzyme converts the substrates into different molecules known as products. Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life.[1]:8.1 Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and a new field of pseudoenzyme analysis has recently grown up, recognising that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties.[2][3] Enzymes are known to catalyze more than 5,000 biochemical reaction types.[4] Most enzymes are proteins, although a few are catalytic RNA molecules. The latter are called ribozymes
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Enzyme
Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate chemical reactions. The molecules upon which enzymes may act are called substrates and the enzyme converts the substrates into different molecules known as products. Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life.[1]:8.1 Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and a new field of pseudoenzyme analysis has recently grown up, recognising that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties.[2][3] Enzymes are known to catalyze more than 5,000 biochemical reaction types.[4] Most enzymes are proteins, although a few are catalytic RNA molecules. The latter are called ribozymes
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Phosphotyrosine
Tyrosine
Tyrosine
(symbol Tyr or Y[1]) or 4-hydroxyphenylalanine is one of the 20 standard amino acids that are used by cells to synthesize proteins. It is a non-essential amino acid with a polar side group. Its codons are UAC and UAU. The word "tyrosine" is from the Greek tyros, meaning cheese, as it was first discovered in 1846 by German chemist Justus von Liebig in the protein casein from cheese.[2][3] It is called tyrosyl when referred to as a functional group or side chain
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Tyrosine Kinase
A tyrosine kinase is an enzyme that can transfer a phosphate group from ATP to a protein in a cell. It functions as an "on" or "off" switch in many cellular functions. Tyrosine
Tyrosine
kinases are a subclass of protein kinase. The phosphate group is attached to the amino acid tyrosine on the protein. Tyrosine
Tyrosine
kinases are a subgroup of the larger class of protein kinases that attach phosphate groups to other amino acids (serine and threonine). Phosphorylation
Phosphorylation
of proteins by kinases is an important mechanism in communicating signals within a cell (signal transduction) and regulating cellular activity, such as cell division. Protein
Protein
kinases can become mutated, stuck in the "on" position, and cause unregulated growth of the cell, which is a necessary step for the development of cancer
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Cysteine
Cysteine
Cysteine
(symbol Cys or C)[3] (/ˈsɪstɪiːn/)[4] is a semi-essential[5] proteinogenic amino acid with the formula HO2CCH(NH2)CH2SH. It is encoded by the codons UGU and UGC. The thiol side chain in cysteine often participates in enzymatic reactions, as a nucleophile. The thiol is susceptible to oxidation to give the disulfide derivative cystine, which serves an important structural role in many proteins. When used as a food additive, it has the E number E920. Cysteine
Cysteine
has the same structure as serine, but with one of its oxygen atoms replaced by sulfur; replacing it with selenium gives selenocysteine. (Like other natural proteinogenic amino acids cysteine has (L) chirality in the older D/L notation based on homology to D and L glyceraldehyde
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Arginine
Arginine
Arginine
(symbol Arg or R[1]) is an α-amino acid that is used in the biosynthesis of proteins. It is encoded by the codons CGU, CGC, CGA, CGG, AGA, and AGG.[2] It contains an α-amino group, an α-carboxylic acid group, and a side chain consisting of a 3-carbon aliphatic straight chain ending in a guanidino group
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Adenine
Adenine
Adenine
/ˈædɪnɪn/ (A, Ade) is a nucleobase (a purine derivative). Its derivatives have a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate (ATP) and the cofactors nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD). It also has functions in protein synthesis and as a chemical component of DNA
DNA
and RNA.[2] The shape of adenine is complementary to either thymine in DNA
DNA
or uracil in RNA. The adjacent image shows pure adenine, as an independent molecule. When connected into DNA, a covalent bond is formed between deoxyribose sugar and the bottom left nitrogen, so removing the hydrogen. The remaining structure is called an adenine residue, as part of a larger molecule
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G-proteins
G proteins, also known as guanine nucleotide-binding proteins, are a family of proteins that act as molecular switches inside cells, and are involved in transmitting signals from a variety of stimuli outside a cell to its interior. Their activity is regulated by factors that control their ability to bind to and hydrolyze guanosine triphosphate (GTP) to guanosine diphosphate (GDP). When they are bound to GTP, they are 'on', and, when they are bound to GDP, they are 'off'. G proteins belong to the larger group of enzymes called GTPases. There are two classes of G proteins. The first function as monomeric small GTPases, while the second function as heterotrimeric G protein complexes
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Structural Motif
In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which also appears in a variety of other molecules. Motifs do not allow us to predict the biological functions: they are found in proteins and enzymes with dissimilar functions. Because the relationship between primary structure and tertiary structure is not straightforward, two biopolymers may share the same motif yet lack appreciable primary structure similarity. In other words, a structural motif does not have to be associated with a sequence motif. Also, the existence of a sequence motif does not necessarily imply a distinctive structure
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