Catabolism activator protein (2023)

Catabolite activating protein in complex with DNA and cAMP (1J59).Escherichia coli

Catabolite activating proteinEscherichia coli(PDB ID = 1J59) is a transcription activating protein that binds, in the presence of the allosteric effector, cAMP, to specific DNA sites located in operons to activate or inhibit DNA transcription from a nearby promoter (1). Studying CAP is critical to understanding the mechanism by which CAP enhances gene expression and transcriptional regulation of several genes functionally linked by a common signal (2). These CAP functions depend on CAP structural features and CAP-DNA binding. The CAP structure allows the protein to interact with its allosteric effector cAMP and the DNA molecule. CAP-DNA binding is a significant indicator of the role of DNA bending in creating the specific hydrogen-bonding interactions that ensure the stability of the complex.

The catabolite activator protein has a length of 209 residues and a molecular weight of 44603.02 Da (3). Its isoelectric point is 8.56, indicating that the primary structure contains more basic than acidic amino acids and that the protein has a net positive charge at physiological pH (4). CAP consists of two symmetrical subunits consisting of the same sequence of 209 amino acids. Each subunit contains large areas of positive potential that attach to the negatively charged phosphate backbone of the DNA. This bends the DNA up to 150°, which is necessary for CAP to interact with the entire 28 bp binding site found in DNA (1). Without this conformational change in DNA, the increased distance between DNA bases and CAP amino acid residues would not allow for the formation of stabilizing hydrogen bonds and van der Waals interactions.

(Video) Catabolite Activator Protein: Catabolite Repression

The secondary structure of the two CAP subunits consists of beta sheets, alpha helices, 3/10 helices, and random turns. The structural stability provided by the appropriate hydrogen bonds between the amino acid residues in the alpha helices and beta sheets maintains the conformation of the CAP, which is essential for precise DNA interactions. Although less common, and in some cases irregular, the hydrogen bonding interactions in 3/10 helices and random coils also contribute to the structural stability of CAPs. The secondary structure is further characterized by the helix-turn-helix DNA binding motif (5). This motif consists of two alpha helices joined by a short chain of amino acids and is found in many transcription-regulating proteins (6). One of the alpha helices is at the C-terminus of the motif, while the other alpha helix is ​​at the N-terminus. The C-terminal alpha helix contributes to DNA recognition by binding to the DNA major groove through hydrogen bonding and van der Waals interactions. The N-terminal alpha helix stabilizes the DNA-protein interaction through the same intermolecular forces. In the CAP protein, there are two helix-turn-helix motifs in the DNA binding region. One is outside the A subunit and the other symmetrically on the B subunit. Each of them consists of two alpha helices connected by an area of ​​random turns. These structural features enable hydrogen bonding between amino acid residues that provide the stability and specificity of the CAP DNA binding site.

Specific hydrogen bonding interactions are important for achieving a sharp DNA bend in the CAP-DNA binding complex. In this complex, the DNA molecule wraps around the sides of the CAP. One CAP subunit interacts with half of the DNA binding site, while the other subunit interacts with the remaining half. Arg-180, Glu-181 and Arg-185 with CAP form hydrogen bonds with the edges of DNA bases (5). The Arg-180 guanidine side chain in complex A forms hydrogen bonds with the O6 and N7 atoms of G5. In complex B, Arg-180 forms a symmetrical hydrogen bond with G18'. The carboxylate side chain of Glu-181 hydrogen bonds with the C7' nitrogen of complex A and the C16 nitrogen of complex B. Finally, Arg-185 hydrogen bonds via water to T15 in complex B. A and G14 in complex B. The formation of these hydrogen bonding is important for the stability of the CAP-DNA complex.

(Video) Catabolite Repression | cAMP, CAP, Glucose and Lac Operon.

Arg-180, Glu-181 and Arg-185 are functionally important residues due to their ability to recognize and bind to three of the four most conserved base pairs at the DNA binding site: G•C base pair 5, G•C base pair 7 and base pair A •T 8. Removal of the Arg-180 and Glu-181 side chains results in loss of binding specificity at base pair positions 5 and 7, respectively (5). This suggests that the nitrogen-hydrogen bond of the guanidinium side chain of Arg-180 and the oxygen-hydrogen bond of the carboxylic side chain of Glu-181 are essential hydrogen bond donors without which stable DNA-protein interactions would not occur. These highly conserved amino acids are therefore essential for the formation of CAP-DNA complexes through direct reading or direct hydrogen bonding interactions between amino acids and DNA base pairs. CAP also forms hydrogen bond interactions between amino acids and the DNA phosphate backbone. Specifically, these interactions include Ser-179 and Thr-182. In the A and B subunits, the side chain hydroxyl groups of Ser-179 and Thr-182 form hydrogen bonds with the negatively charged phosphates of nucleotides 9' and 14 (5). The hydroxyl groups of these highly conserved amino acids are therefore required for stable CAP-DNA binding.

CAP binds to the cofactor, cyclic adenosine-3',5'-monophosphate (cAMP), acquiring the ability to bind DNA and regulate transcription. cAMP binds to CAP via direct water-mediated hydrogen bonding. The carbonyl chain of Glu-81 and the amide group of Gln-125 interact with a water molecule that is hydrogen-bonded to the phosphate group of cAMP (7). The side chain hydroxyl groups of Thr-127 and Ser-83 interact with two water molecules that are hydrogen-bonded to N1 and N7 of the adenine residue. The 2'-OH cAMP forms hydrogen bonds with the side chains of Gly-71 and Glu-72 in the binding pocket formed by residues 70 to 73. Leu-73 and the connected rings of the adenine residue participate in hydrophobic interactions according to Van der Waals. Together, these hydrogen bonds and van der Waals interactions ensure the stability and longevity of cAMP binding. These features are important because cAMP acts as an allosteric effector mediating CAP binding. The intracellular concentration of cAMP varies in response to different nutritional conditions in the extracellular environment. CAP can then regulate the expression of genes encoding catabolic enzymes needed to metabolize various nutrients. For example, in the presence of glucose, the intracellular concentration of cAMP decreases, inhibiting the transcription of the lac operon (8). This causes the cell to metabolize available glucose instead of lactose as a source of carbon and energy.

(Video) Lac Operon Regulation - Catabolite Repression: Role of cAMP, CAP & Glucose

Studies involving mutant CAP molecules have shown that DNA binding depends on specific amino acid residues. For example, hydrogen bonding between the oxygen and nitrogen atoms of DNA, the Arg-180 guanidine side chain, and the Glu-181 carboxylate side chain is required for stable DNA binding (9). Mutations resulting in amino acid substitutions at position 181 of the CAP have shown that the hydrogen bond between the carboxylate side chain of Glu-181 and the C7' and C16 nitrogen atoms is critical for direct binding to DNA (10). In addition, studies of alternative amino acid sequences in the protein's DNA binding site have shown that the GNGA sequence is important for specific DNA binding (9). A mutation in this sequence results in a loss of the ability to express genes for catabolic enzymes. As a result, the cell cannot metabolize certain nutrients when they are available in the extracellular environment. This consequence demonstrates the importance of sequence specific binding to the CAP protein and for bacterial survival,Escherichia coli.

When the CAP sequence is compared with other primary protein structures via the PBLAST database, the cAMP receptor protein (CRP) of the CRP/FNR family of bacteria,Mycobacterium tuberculosis(PDB ID = 3I54), has a remarkably similar sequence (11). Both structures bind to the cyclic adenosine-3',5'-monophosphate ligand or cAMP and are responsible for the activation and repression of transcription. Like CAP, cAMP acts as an allosteric effector with CRP, changing the conformation of the protein to allow binding to DNA. Both proteins contain a helix-turn-helix motif involved in DNA binding. Since the CRP protein is sequence-like with 249 amino acids and a low E value of 5e-21 (or 5 x 10^-21), the original CAP structure may be genetically conserved intuberculosis. A low E value indicates a similar primary structure. Using Dali's tertiary structure comparison server, the transcription regulator showed similarity with a Z score of 21.9 (12). A Z-score greater than 2 is significant. The significant difference between CRP and CAP is that CRP consists of four identical subunits, each of which binds to a cAMP molecule, while CAP has only two identical subunits and can bind to a cAMP molecule. The presence of additional subunits suggests a more extensive DNA binding site when the protein is allosterically activated by cAMP, suggesting that the PCR function involves the regulation of transcription by binding a longer DNA sequence.

(Video) Catabolic Activator Protein (CAP) & Inducer Operon (LAC Operon)

Regulator of virulence factorsPseudomonas aeruginosa(PDB ID = 2OZ6) also showed a significant similarity to the tertiary structure of the CAP with a Z score of 28.4 (12). Like CAP, the virulence factor regulator is a symmetrical protein that binds to DNA and acts as a global regulator of transcription (13). cAMP also acts as an allosteric effector that allows DNA to bind to the two sites containing the helix-turn-helix motif, as is the case in both PCR CAP and M. tuberculosis. Based on the low E value of the protein, 4e-97 (4 x 10^-97), it can be determined that the 207 amino acid primary structure of the virulence factor regulator is also remarkably similar to the 209 amino acid primary structure of CAP. (11). Unlike CAP and CRP, the virulence factor consists of one subunit and binds two molecules of cAMP, as opposed to one molecule for CAP and four molecules for CRP. A single PCR subunit suggests a less extensive DNA binding site and consequently a shorter DNA binding sequence. Therefore, the regulation of transcription by CRP is mediated by the maintenance of a less extensive DNA sequence than the regulation of transcription by CAP.

In summary, catabolite activating protein is a transcription activating protein that binds to the allosteric effector cAMP to gain DNA binding capacity. DNA binding is facilitated by the resulting structure of the amino acid sequence of the protein. The secondary structure of the CAP provides structural stability through hydrogen bond interactions and provides two binding sites for the coil-coil motif to the DNA. Hydrogen bonds and van der Waals interactions facilitate the stable binding of cAMP when present in the intracellular environment, allowing conformation change and DNA binding. The specific hydrogen bonding interactions through the amino acid side chains of the CAP ensure the stability and specificity of the interaction with the highly conserved DNA binding sequence. The similarities between the CAP, the cAMP receptor protein and the virulence factor regulator show that the preservation of the primary and tertiary amino acid structure can be an indicator of the similarity of protein function, since all these proteins are involved in the regulation of transcription. The specificity of the CAP structure and the preservation of its amino acid sequence are essential for proper interactions between proteins, cAMP and DNA, and for the regulation of transcription, which indicates an important relationship between protein structure and function.

(Video) Ubiquitination of Proteins and Protein Degradation

(Video) Introducing CAP (Catabolite Activator Protein)


Catabolism activator protein? ›

Catabolite activator protein

Catabolite activator protein
cAMP receptor protein (CRP; also known as catabolite activator protein, CAP) is a regulatory protein in bacteria. CRP protein binds cAMP, which causes a conformational change that allows CRP to bind tightly to a specific DNA site in the promoters of the genes it controls. › wiki › CAMP_receptor_protein
(CAP), also known as cyclic AMP
cyclic AMP
Cyclic adenosine monophosphate (cAMP, cyclic AMP, or 3',5'-cyclic adenosine monophosphate) is a second messenger, or cellular signal occurring within cells, that is important in many biological processes. › Cyclic_adenosine_monophosphate
receptor protein (CRP), is activated by cyclic AMP and stimulates synthesis of the enzymes that break down non-glucose food molecules. It is composed of two identical subunits, shown here in blue from PDB
RCSB PDB ( is the US data center for the global Protein Data Bank (PDB) archive of 3D structure data for large biological molecules (proteins, DNA, and RNA) essential for research and education in fundamental biology, health, energy, and biotechnology. › pages › about-us
entry 1cgp .

Which is catabolite activator protein? ›

The catabolite activator protein (CAP, also known as cAMP receptor protein, CRP) is a transcriptional activator, present as homodimer in solution, each subunit including a ligand-binding domain at the N-terminus and a DNA-binding domain at the C-terminus.

What is catabolite activator protein in biology? ›

A catabolite activator protein (CAP) is a protein homodimer in solution (a macromolecule made up of two non-covalently linked protein subunits), also known as a cAMP receptor protein, which acts as an activator of DNA transcription.

How is a catabolite activator protein regulated? ›

Regulation of Transcription in Prokaryotes

The Crp protein is allosteric. In order to bind DNA and activate genes, it must first bind its signal molecule, cyclic AMP. When Crp binds cyclic AMP, it forms dimers and these can bind to a recognition site in the DNA upstream of the promoter.

What is the catabolite activator protein in the lac operon? ›

The lac repressor senses lactose indirectly, through its isomer allolactose. Catabolite activator protein (CAP) acts as a glucose sensor. It activates transcription of the operon, but only when glucose levels are low. CAP senses glucose indirectly, through the "hunger signal" molecule cAMP.

What is an example of an activator protein? ›

One example of an activator is the protein CAP. In the presence of cAMP, CAP binds to the promoter and increases RNA polymerase activity. In the absence of cAMP, CAP does not bind to the promoter. Transcription occurs at a low rate.

What do activator proteins do? ›

A transcriptional activator is a protein (transcription factor) that increases transcription of a gene or set of genes. Activators are considered to have positive control over gene expression, as they function to promote gene transcription and, in some cases, are required for the transcription of genes to occur.

What is the purpose of catabolite activation of gene expression? ›

When glucose levels decline in the cell, accumulating cAMP binds to the positive regulator catabolite activator protein (CAP), a protein that binds to the promoters of operons that control the processing of alternative sugars, such as the lac operon. The CAP assists in production in the absence of glucose.

Is catabolite activator protein an inducer? ›

Catabolite Activator Protein (CAP): An Activator Regulator

Just as the trp operon is negatively regulated by tryptophan molecules, there are proteins that bind to the operator sequences that act as a positive regulator to turn genes on and activate them. For example, when glucose is scarce, E.

What does catabolite repression protein do? ›

Catabolite repression control (Crc) protein, a global translational repressor, is involved in the regulation of metabolism of secondary carbon sources.

What type of control is catabolite repression? ›

Catabolite repression is considered to be a part of global control system and therefore it affects more genes rather than just lactose gene transcription.

What is the importance of catabolite repression in bacteria? ›

Carbon catabolite repression (CCR) in bacteria is generally regarded as a regulatory mechanism to ensure sequential utilization of carbohydrates. Selection of the carbon sources is mainly made at the level of carbohydrate-specific induction.

What does catabolite repression inhibit? ›

In classical catabolite repression, transport of glucose leads to dephosphorylation of IIAGlc of the phosphoenolpyruvate:sugar phosphotransferase system, which prevents this protein from activating membrane-bound adenylate cyclase (Cya).

How does catabolite control the lac operon? ›

Catabolite repression is positive control of the lac operon. The effect is an increase in the rate of transcription. In this case, the CAP protein is activated by cAMP to bind to the lac operon and facilitate the binding of RNA polymerase to the promoter to transcribe the genes for lactose utilization.

What is the role of catabolite repression in the lac operon? ›

CAP acts as a sensor for glucose. It activates transcription of the operon but only when glucose levels are low. CAP senses glucose indirectly through the 'hunger signal' molecule cAMP which is a central regulator to different nutrients in environment such as glucose.

What is the catabolite activator protein CAP in E coli? ›

Catabolite Activator Protein. The catabolite activator protein (CAP), also known as the cyclic AMP (cAMP) receptor protein (CRP), is a positive transcriptional activator in E. coli. CAP activates transcription at a variety of promoters that drive operons involved in catabolite metabolism (e.g. Plac, Pgal).

What is the role of activator protein in gene expression? ›

Transcriptional activators are required to turn on the expression of genes in a eukaryotic cell. Activators bound to the enhancer can facilitate either the recruitment of RNA polymerase II to the promoter or its elongation.

What are types of activators in enzymes? ›

Enzyme activators are chemical compounds that increase a velocity of enzymatic reaction. Their actions are opposite to the effect of enzyme inhibitors. Among activators we can find ions, small organic molecules, as well as peptides, proteins, and lipids.

Is repressor protein the same as activator protein? ›

When is a Repressor an Activator? According to the conventional wisdom, transcription factors are typically classified as “activators” or “repressors”. Activators recruit coactivators, resulting in gene activation, while repressors recruit corepressors, leading to transcriptional repression.

Does an activator protein decrease transcription of a gene? ›

Transcription factors that are activators boost a gene's transcription. Repressors decrease transcription. Groups of transcription factor binding sites called enhancers and silencers can turn a gene on/off in specific parts of the body.

Do activator proteins bind to operator? ›

Repressors and activators are proteins produced in the cell. Both repressors and activators regulate gene expression by binding to specific DNA sites adjacent to the genes they control. In general, activators bind to the promoter site, while repressors bind to operator regions.

What are activators and enhancers? ›

enhancer: a short region of DNA that can increase transcription of genes. repressor: any protein that binds to DNA and thus regulates the expression of genes by decreasing the rate of transcription. activator: any chemical or agent which regulates one or more genes by increasing the rate of transcription.

What activates gene expression? ›

Signals from the environment or from other cells activate proteins called transcription factors. These proteins bind to regulatory regions of a gene and increase or decrease the level of transcription.

What is the difference between an activator and an inducer? ›

Activators bind to the promoter to enhance the binding of RNA polymerase. Inducer molecules can increase transcription either by inactivating repressors or by activating activator proteins.

Does catabolite repression inhibit Lactose? ›

Extracellular glucose affects the lactose operon activation by inhibiting the production of cAMP (catabolite repression) and by reducing the efficiency of lactose permease to transport lactose molecules into the cell (inducer exclusion).

Why is protein catabolism important? ›

Clinical Significance

Proper functioning of protein catabolism is of utmost importance to sustain the metabolic needs of the human body. The breakdown of large polypeptide chains to unleash free essential and non-essential amino acids provides cells with the needed substrates for protein synthesis or energy creation.

What causes protein catabolism? ›

Accelerated protein catabolism in uremia occurs in animals and patients with acute (ARF) and chronic renal failure (CRF). Possible causes include resistance to both insulin-induced inhibition of protein-degradation and insulin-induced stimulation of protein synthesis. The mechanisms for these effects are unknown.

How are proteins Catabolized? ›

Protein Catabolism

Proteins are degraded through the concerted action of a variety of microbial protease enzymes. Extracellular proteases cut proteins internally at specific amino acid sequences, breaking them down into smaller peptides that can then be taken up by cells.

How does catabolite repression allow cells to save energy? ›

Ans : Catabolite repression helps the microorganism to adapt faster within the available energy source. This mechanism is achieved by enzyme synthesis that involves carbon sources catabolism. In simpler terms, Catabolite repression refers to metabolite control exertion on the synthesis rate of specific enzymes.

What is the preferred energy source in catabolite repression? ›

This process is called carbon catabolite repression. The Gram-positive bacterium Bacillus subtilis uses glucose as the preferred source of carbon and energy. Glucose-mediated catabolite repression is caused by binding of the CcpA transcription factor to the promoter regions of catabolic operons.

What is a catabolite? ›

catabolite. / (kəˈtæbəˌlaɪt) / noun. a substance produced as a result of catabolism.

How do you overcome catabolite repression? ›

To overcome catabolite repression, industrial fermentation processes are usually operated in substrate-limited fed-batch mode.

What is catabolite repression in biology? ›

System of gene control in some bacterial operons in which glucose is used preferentially and the metabolism of other sugars is repressed in the presence of glucose.

Is catabolite repression negative control? ›

The implication from these results is that in contrast to catabolite repression in Escherichia coli, which is mediated by catabolite-activating protein (CAP), catabolite repression in yeast occurs by a negative control mechanism involving a putative repressor protein.

What protein represses the lac operon? ›

The lac operon is repressed by LacI, encoded by lacI. The lacI gene is upstream of lacZYA and faces in the opposite direction. The repressor, LacI, binds to the operator sequence upstream of lacZYA and prevents transcription of those genes unless the inducer molecule is present.

Which protein activates transcription in E. coli? ›

E. coli Fis protein activates ribosomal RNA transcription in vitro and in vivo.

What is the protein that kills sensitive E. coli cells? ›

Colicins, produced by and toxic to Escherichia coli bacteria are three-domain proteins so efficient that one molecule can kill a cell.

Is Gal4 an activator protein? ›

One of the earliest model systems for studying transcriptional regulation was that of the galactose-mediated induction of gene expression in yeast, which is under the control of the transcriptional activator Gal4.

What is catabolite repressor protein? ›

The catabolite repressor protein (CRP) positively regulated csgD transcription, leading to curli and cellulose production in the UPEC isolate, UTI89. Glucose, a known inhibitor of CyaA activity, blocked extracellular matrix formation when added to the growth medium.

Is GCN4 a transcriptional activator? ›

GCN4 is a transcriptional activator in the bZIP family that regulates amino acid biosynthetic genes in the yeast Saccharomyces cerevisiae.

What is Gal4 used for? ›

The GAL4-UAS system is a biochemical method used to study gene expression and function in organisms such as the fruit fly.

Is catabolite activator protein an enzyme? ›

Catabolite activator protein (CAP), also known as cyclic AMP receptor protein (CRP), is activated by cyclic AMP and stimulates synthesis of the enzymes that break down non-glucose food molecules. It is composed of two identical subunits, shown here in blue from PDB entry 1cgp .

What is the purpose of Gal4? ›

The Gal4/UAS system

It is a Drosophila geneticist's main workhorse to turn genes on or off. Gal4 is a transcriptional activator that binds to UAS enhancer sequences found in DNA. It then recruits transcription machinery to the site to induce gene expression.

What is an example of a catabolite repressor? ›

For example, if E. coli is placed on an agar plate containing only glucose and lactose, the bacteria will use glucose first and lactose second. When glucose is available in the environment, the synthesis of β-galactosidase is under repression due to the effect of catabolite repression caused by glucose.

Does creb activate transcription? ›

One of the best characterized stimulus-induced transcription factors, cyclic AMP response element (CRE)-binding protein (CREB), activates transcription of target genes in response to a diverse array of stimuli, including peptide hormones, growth factors, and neuronal activity, that activate a variety of protein kinases ...

What are the 3 transcriptional activation domains? ›

∑ Transcription activation domains include acidic domains, glutamine rich domains and proline rich domains.

What are transcription activator like proteins? ›

Transcription activator-like effectors (TALEs) are proteins secreted by Xanthomonas bacteria to aid the infection of plant species. TALEs assist infections by binding to specific DNA sequences and activating the expression of host genes.

What is catabolite repression mediated by? ›

Catabolite repression mediated by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analyses.

What is catabolite repression in eukaryotes? ›

In microbial eukaryotes, carbon catabolite repression (CCR) mediates the preferential utilization of glucose, primarily by repressing alternate carbon source utilization.


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