Biotin carboxylase | |||||||||
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Identifiers | |||||||||
EC no. | 6.3.4.14 | ||||||||
CAS no. | 9075-71-2 | ||||||||
Databases | |||||||||
IntEnz | IntEnz view | ||||||||
BRENDA | BRENDA entry | ||||||||
ExPASy | NiceZyme view | ||||||||
KEGG | KEGG entry | ||||||||
MetaCyc | metabolic pathway | ||||||||
PRIAM | profile | ||||||||
PDB structures | RCSB PDB PDBe PDBsum | ||||||||
Gene Ontology | AmiGO / QuickGO | ||||||||
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Biotin carboxylase C-terminal domain | |||||||||
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Identifiers | |||||||||
Symbol | Biotin_carb_C | ||||||||
Pfam | PF02785 | ||||||||
InterPro | IPR005482 | ||||||||
SCOP2 | 1dv1 / SCOPe / SUPFAM | ||||||||
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In enzymology, a biotin carboxylase (EC 6.3.4.14) is an enzyme that catalyzes the chemical reaction
The three substrates of this enzyme are ATP, biotin-carboxyl-carrier protein (BCCP), and CO2, whereas its three products are ADP, phosphate, and carboxybiotin-carboxyl-carrier protein.
The systematic name of this enzyme class is biotin-carboxyl-carrier-protein:carbon-dioxide ligase (ADP-forming). This enzyme is also called biotin carboxylase (component of acetyl CoA carboxylase). This enzyme participates in fatty acid biosynthesis. This enzyme participates in fatty acid biosynthesis by providing one of the catalytic functions of the Acetyl-CoA carboxylase complex. As previously mentioned, after the carboxybiotin product is formed, the carboxyltransferase unit of the complex will transfer the activated carboxy group from BCCP to Acetyl-CoA, forming a malonate analog known as malonyl-CoA. Malonyl-CoA serves as the primary carbon donor in fatty acid biosynthesis, followed by a series of reduction and dehydration reactions to remove the acyl group. [1]
Biotin carboxylases are a conserved enzyme present within biotin-dependent carboxylase complexes such as acetyl-CoA carboxylase. How biotin carboxylase functions is, within the relevant carboxylase complex, there is a biotin carboxyl-carrier protein which is covalently linked to biotin via a Lys-residue. [2] Both biotin carboxylase activity as well as the BCCP within the carboxylase complex are highly conserved among this enzyme class. The main source of variation for carboxylases arises from the carboxyltransferase component, as the molecule to which the carboxyl group is transferred (from biotin) dictates the necessary specificity component to catalyze this transfer.
The structure of biotin carboxylase heavily influences the reaction pathway the enzyme catalyzes, so discussion of this reaction pathway must also touch on how the substrates and intermediates are stabilized within the active site. Bicarbonate (HCO3−) is held within the active site of biotin carboxylase by hydrogen bonding with biotin as well as a bidentate ion pair interaction of the negatively charged oxygen's with Arg292 iminium ion. [2] It is hypothesized that the Glu296 residue of B.C. acts as a base, deprotonating bicarbonate molecule, thus facilitating nucleophilic attack of the carbonyl-oxygen on the terminal phosphate molecule of ATP. This initial reaction of the pathway can happen because the ATP is also held tightly within the active site pocket via non-covalent coordination of ATP with magnesium ions.
After this nucleophilic attack, the carbonate molecule is degraded to CO2 via electron pushing, producing a PO43- ion which then acts as a base and deprotonates the amide of the ureido ring within biotin. An enolate-like intermediate is formed, producing a negative charge on the oxygen, which is stabilized by the iminium ion of Arg338. The enolate then executes a nucleophilic attack on CO2 (which is being held in place through H-bonding with Glu296 residue), ultimately leading to the product of this enzymatic pathway: carboxybiotin. [2] After this reaction occurs, the carboxyltransferase enzyme present within the complex acts upon the carboxybiotin to transfer the carboxyl group to the target acceptor molecule i.e. acetyl Co-A, propionyl Co-A etc.
As of late 2007 [update] , 5 structures have been solved for this class of enzymes, with PDB accession codes 1BNC, 1DV1, 1DV2, 2GPS, and 2GPW.
The crystal structure has been determined for the biotin carboxylase (acetyl-CoA carboxylase) of Escherichia coli, but the eukaryotic B.C. is difficult to obtain info on as it is catalytically inactive in solution. E. coli biotin carboxylase is composed of two homogenous dimers made up of 3 domains: A, B, and C. [2] It is believed that the B domain of each monomer is essential to the function of this enzyme, as there is extreme flexibility of this domain seen in the crystal structure. Upon binding of the ATP substrate, a conformational change occurs where the B domain essentially closes over the active site. While this change is thought to bring ATP within close enough proximity for the reaction to occur, the active site was still solvent exposed. Because of this anomaly in the crystal structure, it is believed that the attachment of biotin to BCCP aids in this reaction pathway, essentially covering biotin within the active site, as evidence shows free biotin is not as great of a substrate for this enzyme when compared to biotin-BCCP. [3] A C-terminal conserved domain within this enzyme contains most of the active site residues. [4] The Glu296 and Arg338 are highly conserved residues among this subclass of enzymes, and work to stabilize the reaction intermediates and keep them within the active site pocket until the carboxylation is complete. [3]
This enzyme is vital to life and has maintained its function across a variety of organisms. While the structure itself may be divergent based on the biotin carboxylase function and which complex it is present in, the enzyme still works to serve the same function. Fatty acid synthesis provides sterols and other lipids essential to biochemical pathways, and the necessity for this enzyme function is confirmed by the highly conserved active site amino acid sequence. [2]
Coenzyme A (CoA, SHCoA, CoASH) is a coenzyme, notable for its role in the synthesis and oxidation of fatty acids, and the oxidation of pyruvate in the citric acid cycle. All genomes sequenced to date encode enzymes that use coenzyme A as a substrate, and around 4% of cellular enzymes use it (or a thioester) as a substrate. In humans, CoA biosynthesis requires cysteine, pantothenate (vitamin B5), and adenosine triphosphate (ATP).
In molecular biology, biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds, or joined to form macromolecules. This process often consists of metabolic pathways. Some of these biosynthetic pathways are located within a single cellular organelle, while others involve enzymes that are located within multiple cellular organelles. Examples of these biosynthetic pathways include the production of lipid membrane components and nucleotides. Biosynthesis is usually synonymous with anabolism.
Pyruvate carboxylase (PC) encoded by the gene PC is an enzyme of the ligase class that catalyzes the physiologically irreversible carboxylation of pyruvate to form oxaloacetate (OAA).
Acetyl-CoA carboxylase (ACC) is a biotin-dependent enzyme that catalyzes the irreversible carboxylation of acetyl-CoA to produce malonyl-CoA through its two catalytic activities, biotin carboxylase (BC) and carboxyltransferase (CT). ACC is a multi-subunit enzyme in most prokaryotes and in the chloroplasts of most plants and algae, whereas it is a large, multi-domain enzyme in the cytoplasm of most eukaryotes. The most important function of ACC is to provide the malonyl-CoA substrate for the biosynthesis of fatty acids. The activity of ACC can be controlled at the transcriptional level as well as by small molecule modulators and covalent modification. The human genome contains the genes for two different ACCs—ACACA and ACACB.
Biotin carboxyl carrier protein (BCCP) refers to proteins containing a biotin attachment domain that carry biotin and carboxybiotin throughout the ATP-dependent carboxylation by biotin-dependent carboxylases. The biotin carboxyl carrier protein is an Acetyl CoA subunit that allows for Acetyl CoA to be catalyzed and converted to malonyl-CoA. More specifically, BCCP catalyzes the carboxylation of the carrier protein to form an intermediate. Then the carboxyl group is transferred by the transcacrboxylase to form the malonyl-CoA. This conversion is an essential step in the biosynthesis of fatty acids. In the case of E. coli Acetyl-CoA carboxylase, the BCCP is a separate protein known as accB. On the other hand, in Haloferax mediterranei, propionyl-CoA carboxylase, the BCCP pccA is fused with biotin carboxylase.
Phosphoenolpyruvate carboxylase (also known as PEP carboxylase, PEPCase, or PEPC; EC 4.1.1.31, PDB ID: 3ZGE) is an enzyme in the family of carboxy-lyases found in plants and some bacteria that catalyzes the addition of bicarbonate (HCO3−) to phosphoenolpyruvate (PEP) to form the four-carbon compound oxaloacetate and inorganic phosphate:
Oxaloacetate decarboxylase is a carboxy-lyase involved in the conversion of oxaloacetate into pyruvate.
Oxidative decarboxylation is a decarboxylation reaction caused by oxidation. Most are accompanied by α- Ketoglutarate α- Decarboxylation caused by dehydrogenation of hydroxyl carboxylic acids such as carbonyl carboxylic acid, malic acid, isocitric acid, etc.
Propionyl-CoA is a coenzyme A derivative of propionic acid. It is composed of a 24 total carbon chain and its production and metabolic fate depend on which organism it is present in. Several different pathways can lead to its production, such as through the catabolism of specific amino acids or the oxidation of odd-chain fatty acids. It later can be broken down by propionyl-CoA carboxylase or through the methylcitrate cycle. In different organisms, however, propionyl-CoA can be sequestered into controlled regions, to alleviate its potential toxicity through accumulation. Genetic deficiencies regarding the production and breakdown of propionyl-CoA also have great clinical and human significance.
Propionyl-CoA carboxylase (EC 6.4.1.3, PCC) catalyses the carboxylation reaction of propionyl-CoA in the mitochondrial matrix. PCC has been classified both as a ligase and a lyase. The enzyme is biotin-dependent. The product of the reaction is (S)-methylmalonyl CoA.
Methylcrotonyl CoA carboxylase is a biotin-requiring enzyme located in the mitochondria. MCC uses bicarbonate as a carboxyl group source to catalyze the carboxylation of a carbon adjacent to a carbonyl group performing the fourth step in processing leucine, an essential amino acid.
The long chain fatty acyl-CoA ligase is an enzyme of the ligase family that activates the oxidation of complex fatty acids. Long chain fatty acyl-CoA synthetase catalyzes the formation of fatty acyl-CoA by a two-step process proceeding through an adenylated intermediate. The enzyme catalyzes the following reaction,
Acetyl-CoA synthetase (ACS) or Acetate—CoA ligase is an enzyme involved in metabolism of acetate. It is in the ligase class of enzymes, meaning that it catalyzes the formation of a new chemical bond between two large molecules.
In molecular biology, Beta-ketoacyl-ACP synthase EC 2.3.1.41, is an enzyme involved in fatty acid synthesis. It typically uses malonyl-CoA as a carbon source to elongate ACP-bound acyl species, resulting in the formation of ACP-bound β-ketoacyl species such as acetoacetyl-ACP.
Thiolases, also known as acetyl-coenzyme A acetyltransferases (ACAT), are enzymes which convert two units of acetyl-CoA to acetoacetyl CoA in the mevalonate pathway.
Pantothenate kinase (EC 2.7.1.33, PanK; CoaA) is the first enzyme in the Coenzyme A (CoA) biosynthetic pathway. It phosphorylates pantothenate (vitamin B5) to form 4'-phosphopantothenate at the expense of a molecule of adenosine triphosphate (ATP). It is the rate-limiting step in the biosynthesis of CoA.
Carbamoyl phosphate synthetase catalyzes the ATP-dependent synthesis of carbamoyl phosphate from glutamine or ammonia and bicarbonate. This enzyme catalyzes the reaction of ATP and bicarbonate to produce carboxy phosphate and ADP. Carboxy phosphate reacts with ammonia to give carbamic acid. In turn, carbamic acid reacts with a second ATP to give carbamoyl phosphate plus ADP.
In enzymology, a [acyl-carrier-protein] S-malonyltransferase is an enzyme that catalyzes the chemical reaction
Fatty-acyl-CoA Synthase, or more commonly known as yeast fatty acid synthase, is an enzyme complex responsible for fatty acid biosynthesis, and is of Type I Fatty Acid Synthesis (FAS). Yeast fatty acid synthase plays a pivotal role in fatty acid synthesis. It is a 2.6 MDa barrel shaped complex and is composed of two, unique multi-functional subunits: alpha and beta. Together, the alpha and beta units are arranged in an α6β6 structure. The catalytic activities of this enzyme complex involves a coordination system of enzymatic reactions between the alpha and beta subunits. The enzyme complex therefore consists of six functional centers for fatty acid synthesis.
The Na+-transporting Carboxylic Acid Decarboxylase (NaT-DC) Family (TC# 3.B.1) is a family of porters that belong to the CPA superfamily. Members of this family have been characterized in both Gram-positive and Gram-negative bacteria. A representative list of proteins belonging to the NaT-DC family can be found in the Transporter Classification Database.