![B12 methylcobalamin](https://upload.wikimedia.org/wikipedia/commons/8/83/B12_methylcobalamin.jpg)
Cobalamin biosynthesis is the process by which
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
and
archea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaeb ...
make
cobalamin
Vitamin B12, also known as cobalamin, is a water-soluble vitamin involved in metabolism. It is one of eight B vitamins. It is required by animals, which use it as a cofactor in DNA synthesis, in both fatty acid and amino acid metabolism. It ...
, vitamin B
12. Many steps are involved in converting
aminolevulinic acid
δ-Aminolevulinic acid (also dALA, δ-ALA, 5ALA or 5-aminolevulinic acid), an endogenous non-proteinogenic amino acid, is the first compound in the porphyrin synthesis pathway, the pathway that leads to heme in mammals, as well as chlorophyll in p ...
via
uroporphyrinogen III
Uroporphyrinogen III is a tetrapyrrole, the first macrocyclic intermediate in the biosynthesis of heme, chlorophyll, vitamin B12, and siroheme. It is a colorless compound, like other porphyrinogens.
Structure
The molecular structure of uroporphyri ...
and adenosylcobyric acid to the final forms in which it is used by
enzymes
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different molecule ...
in both the producing organisms and other species, including humans who acquire it through their diet.
The feature which distinguishes the two main
biosynthetic routes is whether the
cobalt
Cobalt is a chemical element with the symbol Co and atomic number 27. As with nickel, cobalt is found in the Earth's crust only in a chemically combined form, save for small deposits found in alloys of natural meteoric iron. The free element, pr ...
that is at the
catalytic site
In biology and biochemistry, the active site is the region of an enzyme where Enzyme substrate, substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid, amino acid residues that form temporary bonds with t ...
in the
coenzyme
A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's role as a catalyst (a catalyst is a substance that increases the rate of a chemical reaction). Cofactors can be considered "helper molecules" that ass ...
is incorporated early (in
anaerobic organisms
An anaerobic organism or anaerobe is any organism that does not require molecular oxygen for growth. It may react negatively or even die if free oxygen is present. In contrast, an aerobic organism (aerobe) is an organism that requires an oxygenate ...
) or late (in
aerobic organisms
Aerobic means "requiring air," in which "air" usually means oxygen.
Aerobic may also refer to
* Aerobic exercise, prolonged exercise of moderate intensity
* Aerobics, a form of aerobic exercise
* Aerobic respiration, the aerobic process of cell ...
) and whether
oxygen
Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as wel ...
is required. In both cases, the
macrocycle
Macrocycles are often described as molecules and ions containing a ring of twelve or more atoms. Classical examples include the crown ethers, calixarenes, porphyrins, and cyclodextrins. Macrocycles describe a large, mature area of chemistry.
...
that will form a
coordination complex
A coordination complex consists of a central atom or ion, which is usually metallic and is called the ''coordination centre'', and a surrounding array of bound molecules or ions, that are in turn known as ''ligands'' or complexing agents. Many ...
with the cobalt
ion
An ion () is an atom or molecule with a net electrical charge.
The charge of an electron is considered to be negative by convention and this charge is equal and opposite to the charge of a proton, which is considered to be positive by conve ...
is a
corrin
Corrin is a heterocyclic compound. It is the parent macrocycle related to the substituted derivative that is found in vitamin B12. Its name reflects that it is the "core" of vitamin B12 (cobalamins).Nelson, D. L.; Cox, M. M. "Lehninger, Princ ...
ring, specifically one with seven
carboxylate
In organic chemistry, a carboxylate is the conjugate base of a carboxylic acid, (or ). It is an ion with negative charge.
Carboxylate salts are salts that have the general formula , where M is a metal and ''n'' is 1, 2,...; ''carboxylat ...
groups called cobyrinic acid. Subsequently,
amide
In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula , where R, R', and R″ represent organic groups or hydrogen atoms. The amide group is called a peptide bond when it is ...
groups are formed on all but one of the carboxylates, giving cobyric acid, and the cobalt is
ligated by an
adenosyl group. In the final part of the biosynthesis, common to all organisms, an aminopropanol sidechain is added to the one free carboxylic group and assembly of the
nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...
loop, which will provide the second ligand for the cobalt, is completed.
Many
prokaryotic species cannot biosynthesize
adenosylcobalamin
Adenosylcobalamin (AdoCbl), also known as coenzyme B12, cobamamide, and dibencozide, is, along with methylcobalamin (MeCbl), one of the biologically active forms of vitamin B12.
Adenosylcobalamin participates as a cofactor in radical-mediated 1,2 ...
, but can make it from cobalamin which they assimilate from external sources. In humans, dietary sources of cobalamin are bound after ingestion as
transcobalamin
Transcobalamins are carrier proteins which bind cobalamin (B12).
Types
* Transcobalamin I (TCN1), also known as haptocorrin, R-factor, and R-protein, is a glycoprotein produced by the salivary glands of the mouth. It primarily serves to protect ...
s and converted to the coenzyme forms in which they are used.
Cobalamin
Cobalamin (vitamin B
12) is the largest and most structurally complex
vitamin
A vitamin is an organic molecule (or a set of molecules closely related chemically, i.e. vitamers) that is an Nutrient#Essential nutrients, essential micronutrient that an organism needs in small quantities for the proper functioning of its ...
. It consists of a modified
tetrapyrrole
Tetrapyrroles are a class of chemical compounds that contain four pyrrole or pyrrole-like rings. The pyrrole/pyrrole derivatives are linked by ( =- or -- units), in either a linear or a cyclic fashion. Pyrroles are a five-atom ring with four car ...
, a corrin, with a centrally
chelated
Chelation is a type of bonding of ions and molecules to metal ions. It involves the formation or presence of two or more separate coordinate bonds between a polydentate (multiple bonded) ligand and a single central metal atom. These ligands are ...
cobalt ion and is usually found in one of two biologically active forms:
methylcobalamin
Methylcobalamin (mecobalamin, MeCbl, or MeB) is a cobalamin, a form of vitamin B. It differs from cyanocobalamin in that the cyano group at the cobalt is replaced with a methyl group. Methylcobalamin features an octahedral cobalt(III) centre and c ...
and
adenosylcobalamin
Adenosylcobalamin (AdoCbl), also known as coenzyme B12, cobamamide, and dibencozide, is, along with methylcobalamin (MeCbl), one of the biologically active forms of vitamin B12.
Adenosylcobalamin participates as a cofactor in radical-mediated 1,2 ...
. Most
prokaryotes
A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connec ...
, as well as animals, have cobalamin-dependent enzymes that use it as a
cofactor, whereas
plants
Plants are predominantly Photosynthesis, photosynthetic eukaryotes of the Kingdom (biology), kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all curr ...
and
fungi
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
do not use it. In
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
and
archaea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
, these enzymes include
methionine synthase
Methionine synthase also known as MS, MeSe, MTR is responsible for the regeneration of methionine from homocysteine. In humans it is encoded by the ''MTR'' gene (5-methyltetrahydrofolate-homocysteine methyltransferase). Methionine synthase forms ...
,
ribonucleotide reductase
Ribonucleotide reductase (RNR), also known as ribonucleoside diphosphate reductase (rNDP), is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. It catalyzes this formation by removing the 2'-hydroxyl group of th ...
, glutamate and
methylmalonyl-CoA mutase
Methylmalonyl-CoA mutase (, MCM), mitochondrial, also known as methylmalonyl-CoA isomerase, is a protein that in humans is encoded by the ''MUT'' gene. This vitamin B12-dependent enzyme catalyzes the isomerization of methylmalonyl-CoA to succiny ...
s,
ethanolamine ammonia-lyase
The enzyme ethanolamine ammonia-lyase (EC 4.3.1.7) catalyzes the chemical reaction
:ethanolamine \rightleftharpoons acetaldehyde + NH3
This enzyme belongs to the family of lyases, specifically ammonia lyases, which cleave carbon-nitrogen bonds. ...
, and
diol
A diol is a chemical compound containing two hydroxyl groups ( groups). An aliphatic diol is also called a glycol. This pairing of functional groups is pervasive, and many subcategories have been identified.
The most common industrial diol is e ...
dehydratase Dehydratases are a group of lyase enzymes that form double and triple bonds in a substrate through the removal of water. They can be found in many places including the mitochondria, peroxisome and cytosol. There are more than 150 different dehydra ...
.
In certain mammals, cobalamin is obtained through the diet, and is required for methionine synthase and
methylmalonyl-CoA mutase
Methylmalonyl-CoA mutase (, MCM), mitochondrial, also known as methylmalonyl-CoA isomerase, is a protein that in humans is encoded by the ''MUT'' gene. This vitamin B12-dependent enzyme catalyzes the isomerization of methylmalonyl-CoA to succiny ...
.
In humans, it plays essential roles in
folate
Folate, also known as vitamin B9 and folacin, is one of the B vitamins. Manufactured folic acid, which is converted into folate by the body, is used as a dietary supplement and in food fortification as it is more stable during processing and ...
metabolism and in the synthesis of the
citric acid cycle
The citric acid cycle (CAC)—also known as the Krebs cycle or the TCA cycle (tricarboxylic acid cycle)—is a series of chemical reactions to release stored energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins ...
intermediate,
succinyl-CoA
Succinyl-coenzyme A, abbreviated as succinyl-CoA () or SucCoA, is a thioester of succinic acid and coenzyme A.
Sources
It is an important intermediate in the citric acid cycle, where it is synthesized from α-ketoglutarate by α-ketoglutarate de ...
.
Overview of cobalamin biosynthesis
There are at least two distinct cobalamin biosynthetic pathways in
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
:
*
Aerobic
Aerobic means "requiring air," in which "air" usually means oxygen.
Aerobic may also refer to
* Aerobic exercise, prolonged exercise of moderate intensity
* Aerobics, a form of aerobic exercise
* Aerobic respiration, the aerobic process of cellu ...
pathway that requires
oxygen
Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as wel ...
and in which cobalt is inserted late in the pathway;
found in ''
Pseudomonas denitrificans
''Pseudomonas denitrificans'' is a Gram-negative aerobic bacterium that performs denitrification. It was first isolated from garden soil in Vienna, Austria. It overproduces cobalamin ( vitamin B12), which it uses for methionine synthesis and it h ...
'' and ''
Rhodobacter capsulatus
''Rhodobacter capsulatus'' is a species of purple bacteria, a group of bacteria that can obtain energy through photosynthesis. Its name is derived from the Latin adjective "capsulatus" ("with a chest", "encapsulated"), itself derived Latin noun " ...
''.
*
Anaerobic
Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anaerobic may also refer to:
* Anaerobic adhesive, a bonding a ...
pathway in which cobalt insertion is the first committed step towards cobalamin synthesis;
found in ''
Salmonella typhimurium
''Salmonella enterica'' subsp. ''enterica'' is a subspecies of ''Salmonella enterica'', the rod-shaped, flagellated, aerobic, Gram-negative bacterium. Many of the pathogenic serovars of the ''S. enterica'' species are in this subspecies, includi ...
'', ''
Bacillus megaterium
''Bacillus megaterium'' is a rod-like, Gram-positive, mainly aerobic spore forming bacterium found in widely diverse habitats.De Vos, P. ''et al.'' Bergey's Manual of Systematic Bacteriology: Volume 3: The Firmicutes. ''Springer'' (2009) It has ...
'', and ''
Propionibacterium freudenreichii subsp. shermanii''.
Either pathway can be divided into two parts:
*
Corrin
Corrin is a heterocyclic compound. It is the parent macrocycle related to the substituted derivative that is found in vitamin B12. Its name reflects that it is the "core" of vitamin B12 (cobalamins).Nelson, D. L.; Cox, M. M. "Lehninger, Princ ...
ring synthesis leading to cobyrinic acid, with seven
carboxylate
In organic chemistry, a carboxylate is the conjugate base of a carboxylic acid, (or ). It is an ion with negative charge.
Carboxylate salts are salts that have the general formula , where M is a metal and ''n'' is 1, 2,...; ''carboxylat ...
groups. In the anaerobic pathway this already contains cobalt but in the aerobic pathway the material formed at that stage is hydrogenobyrinic acid, without the bound cobalt.
*Insertion of cobalt, where not already present; formation of
amide
In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula , where R, R', and R″ represent organic groups or hydrogen atoms. The amide group is called a peptide bond when it is ...
s on all but one of the carboxylate groups to give cobyric acid; attachment of an
adenosyl group as
ligand
In coordination chemistry, a ligand is an ion or molecule (functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's electr ...
to the cobalt; attachment of an aminopropanol sidechain to the one free carboxylic group and assembly of the
nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...
loop which will provide the second ligand for the cobalt.
A further type of synthesis occurs through a
salvage pathway A salvage pathway is a pathway in which a biological product is produced from intermediates in the degradative pathway of its own or a similar substance. The term often refers to nucleotide salvage in particular, in which nucleotides (purine and py ...
, where outside
corrinoid
Corrinoids are a group of compounds based on the skeleton of corrin, a cyclic system containing four pyrrole rings similar to porphyrins. These include compounds based on octadehydrocorrin, which has the trivial name corrole.
The cobalamins ( vi ...
s are absorbed to make B
12.
Species from the following
genera
Genus ( plural genera ) is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial nomenclat ...
and the following individual species are known to synthesize cobalamin: ''
Propionibacterium
''Propionibacterium'' is a gram-positive, anaerobic, rod-shaped genus of bacteria named for their unique metabolism: They are able to synthesize propionic acid by using unusual transcarboxylase enzymes.
Its members are primarily facultative par ...
shermanii,'' ''
Pseudomonas
''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The members of the genus demonstrate a great deal of metabolic diversity and consequently are able ...
'' ''denitrificans'', ''
Streptomyces
''Streptomyces'' is the largest genus of Actinomycetota and the type genus of the family Streptomycetaceae. Over 500 species of ''Streptomyces'' bacteria have been described. As with the other Actinomycetota, streptomycetes are gram-positive, ...
'' ''griseus'', ''
Acetobacterium
''Acetobacterium'' is a genus of anaerobic, Gram-positive bacteria that belong to the Eubacteriaceae family.
The type species of this genus is ''Acetobacterium woodii''. The name, ''Acetobacterium'', has originated because they are acetogens, ...
'', ''
Aerobacter
''Enterobacter'' is a genus of common Gram-negative, facultatively anaerobic, rod-shaped, non-spore-forming bacteria of the family Enterobacteriaceae. It is the type genus of the order Enterobacterales. Several strains of these bacteria are p ...
'', ''
Agrobacterium
''Agrobacterium'' is a genus of Gram-negative bacteria established by H. J. Conn that uses horizontal gene transfer to cause tumors in plants. ''Agrobacterium tumefaciens'' is the most commonly studied species in this genus. ''Agrobacterium'' is ...
'', ''
Alcaligenes
''Alcaligenes'' is a genus of Gram-negative, Aerobic organism, aerobic, Bacillus (shape), rod-shaped bacteria. The species are motile with amphitrichous flagella and rarely nonmotile. It is a genus of Non-fermenter, non-fermenting bacteria (in t ...
'', ''
Azotobacter
''Azotobacter'' is a genus of usually motile, oval or spherical bacteria that form thick-walled cysts (and also has hard crust) and may produce large quantities of capsular slime. They are aerobic, free-living soil microbes that play an importan ...
'', ''
Bacillus
''Bacillus'' (Latin "stick") is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum ''Bacillota'', with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural ''Bacilli ...
'', ''
Clostridium
''Clostridium'' is a genus of anaerobic, Gram-positive bacteria. Species of ''Clostridium'' inhabit soils and the intestinal tract of animals, including humans. This genus includes several significant human pathogens, including the causative ag ...
'', ''
Corynebacterium
''Corynebacterium'' () is a genus of Gram-positive bacteria and most are aerobe, aerobic. They are bacillus (shape), bacilli (rod-shaped), and in some phases of life they are, more specifically, club (weapon), club-shaped, which inspired the gen ...
'', ''
Flavobacterium
''Flavobacterium'' is a genus of Gram-negative, nonmotile and motile, rod-shaped bacteria that consists of 130 recognized species. Flavobacteria are found in soil and fresh water in a variety of environments. Several species are known to cause ...
'', ''
Lactobacillus
''Lactobacillus'' is a genus of Gram-positive, aerotolerant anaerobes or microaerophilic, rod-shaped, non-spore-forming bacteria. Until 2020, the genus ''Lactobacillus'' comprised over 260 phylogenetically, ecologically, and metabolically diver ...
'', ''
Micromonospora
''Micromonospora'' is a genus of bacteria of the family Micromonosporaceae. They are gram-positive, spore-forming, generally aerobic, and form a branched mycelium; they occur as saprotrophic forms in soil and water. Various species are sources ...
'', ''
Mycobacterium
''Mycobacterium'' is a genus of over 190 species in the phylum Actinomycetota, assigned its own family, Mycobacteriaceae. This genus includes pathogens known to cause serious diseases in mammals, including tuberculosis ('' M. tuberculosis'') and ...
'', ''
Nocardia
''Nocardia'' is a genus of weakly staining Gram-positive, catalase-positive, rod-shaped bacteria. It forms partially acid-fast beaded branching filaments (acting as fungi, but being truly bacteria). It contains a total of 85 species. Some spec ...
'', ''
Proteus
In Greek mythology, Proteus (; Ancient Greek: Πρωτεύς, ''Prōteus'') is an early prophetic sea-god or god of rivers and oceanic bodies of water, one of several deities whom Homer calls the "Old Man of the Sea" ''(hálios gérôn)''. ...
'',
''
Rhizobium
''Rhizobium'' is a genus of Gram-negative soil bacteria that fix nitrogen. ''Rhizobium'' species form an endosymbiotic nitrogen-fixing association with roots of (primarily) legumes and other flowering plants.
The bacteria colonize plant cells ...
'', ''
Salmonella
''Salmonella'' is a genus of rod-shaped (bacillus) Gram-negative bacteria of the family Enterobacteriaceae. The two species of ''Salmonella'' are ''Salmonella enterica'' and ''Salmonella bongori''. ''S. enterica'' is the type species and is fur ...
'', ''
Serratia
''Serratia'' is a genus of Gram-negative, facultatively anaerobic, rod-shaped bacteria of the family Yersiniaceae. According to the List of Prokaryotic names with Standing Nomenclature (LPSN), there are currently 19 species of ''Serratia'' that ar ...
'', ''
Streptococcus
''Streptococcus'' is a genus of gram-positive ' (plural ) or spherical bacteria that belongs to the family Streptococcaceae, within the order Lactobacillales (lactic acid bacteria), in the phylum Bacillota. Cell division in streptococci occurs ...
'' and ''
Xanthomonas
''Xanthomonas'' (from greek: ''xanthos'' – “yellow”; ''monas'' – “entity”) is a genus of bacteria, many of which cause plant diseases. There are at least 27 plant associated ''Xanthomonas spp.'', that all together infect at least 400 ...
''.
Detail of steps up to formation of uroporphyrinogen III
In the early steps of the biosynthesis, a
tetrapyrrolic structural framework is created by the enzymes
deaminase
Deamination is the removal of an amino group from a molecule. Enzymes that catalyse this reaction are called deaminases.
In the human body, deamination takes place primarily in the liver, however it can also occur in the kidney. In situations of ...
and
cosynthetase which transform
aminolevulinic acid
δ-Aminolevulinic acid (also dALA, δ-ALA, 5ALA or 5-aminolevulinic acid), an endogenous non-proteinogenic amino acid, is the first compound in the porphyrin synthesis pathway, the pathway that leads to heme in mammals, as well as chlorophyll in p ...
via
porphobilinogen
Porphobilinogen (PBG) is an organic compound that occurs in living organisms as an intermediate in the biosynthesis of porphyrins, which include critical substances like hemoglobin and chlorophyll.
The structure of the molecule can be described a ...
and
hydroxymethylbilane
Hydroxymethylbilane, also known as preuroporphyrinogen, is an organic compound that occurs in living organisms during the synthesis of porphyrins, a group of critical substances that include haemoglobin, myoglobin, and chlorophyll. The name is ofte ...
to
uroporphyrinogen III
Uroporphyrinogen III is a tetrapyrrole, the first macrocyclic intermediate in the biosynthesis of heme, chlorophyll, vitamin B12, and siroheme. It is a colorless compound, like other porphyrinogens.
Structure
The molecular structure of uroporphyri ...
. The latter is the first
macrocyclic
Macrocycles are often described as molecules and ions containing a ring of twelve or more atoms. Classical examples include the crown ethers, calixarenes, porphyrins, and cyclodextrins. Macrocycles describe a large, mature area of chemistry.
...
intermediate common to
haem
Heme, or haem (pronounced / hi:m/ ), is a precursor to hemoglobin, which is necessary to bind oxygen in the bloodstream. Heme is biosynthesized in both the bone marrow and the liver.
In biochemical terms, heme is a coordination complex "consist ...
,
chlorophyll
Chlorophyll (also chlorophyl) is any of several related green pigments found in cyanobacteria and in the chloroplasts of algae and plants. Its name is derived from the Greek words , ("pale green") and , ("leaf"). Chlorophyll allow plants to a ...
,
sirohaem
Siroheme (or sirohaem) is a heme-like prosthetic group at the active sites of some enzymes to accomplish the six-electron reduction of sulfur and nitrogen. It is a cofactor at the active site of sulfite reductase, which plays a major role in su ...
and cobalamin itself.
Detail of steps from uroporphyrinogen III to acid a,c-diamide in aerobic organisms
The biosynthesis of cobalamin diverges from that of haem and chlorophyll at uroporphrinogen III: its transformation involves the sequential addition of methyl (CH
3) groups to give intermediates that were given
trivial name
In chemistry, a trivial name is a nonsystematic name for a chemical substance. That is, the name is not recognized according to the rules of any formal system of chemical nomenclature such as IUPAC nomenclature of inorganic chemistry, IUPAC inor ...
s according to the number of these groups that have been incorporated. Hence, the first intermediate is precorrin-1, the next is
precorrin-2 and so on. The incorporation of all eight additional methyl groups which occur in cobyric acid was investigated using
13C
methyl-labelled S-adenosyl methionine
''S''-Adenosyl methionine (SAM), also known under the commercial names of SAMe, SAM-e, or AdoMet, is a common cosubstrate involved in methyl group transfers, transsulfuration, and aminopropylation. Although these anabolic reactions occur throug ...
. It was not until scientists at
Rhône-Poulenc Rorer used a
genetically-engineered
Genetic engineering, also called genetic modification or genetic manipulation, is the modification and manipulation of an organism's genes using technology. It is a set of Genetic engineering techniques, technologies used to change the gene ...
strain of ''
Pseudomonas denitrificans
''Pseudomonas denitrificans'' is a Gram-negative aerobic bacterium that performs denitrification. It was first isolated from garden soil in Vienna, Austria. It overproduces cobalamin ( vitamin B12), which it uses for methionine synthesis and it h ...
'', in which eight of the ''cob'' genes involved in the biosynthesis of the vitamin had been
overexpressed, that the complete sequence of methylation and other steps could be determined, thus fully establishing all the intermediates in the pathway.
From uroporphyrinogen III to precorrin-2
The enzyme
CobA
Coba ( es, Cobá) is an ancient Maya city on the Yucatán Peninsula, located in the Mexican state of Quintana Roo. The site is the nexus of the largest network of stone causeways of the ancient Maya world, and it contains many engraved and sculp ...
catalyses two
methylation
In the chemical sciences, methylation denotes the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These t ...
s, to give
precorrin-2:
:
![Dihydrosirochlorin](https://upload.wikimedia.org/wikipedia/commons/6/6c/Dihydrosirochlorin.png)
:(1a) uroporphyrinogen III +
S-adenosyl methionine
''S''-Adenosyl methionine (SAM), also known under the commercial names of SAMe, SAM-e, or AdoMet, is a common cosubstrate involved in methyl group transfers, transsulfuration, and aminopropylation. Although these anabolic reactions occur throug ...
precorrin-1 +
S-adenosyl-L-homocysteine
:(1b) precorrin-1 + S-adenosyl methionine
precorrin-2 + S-adenosyl-L-homocysteine
From precorrin-2 to precorrin-3A
The enzyme
CobI Cobi or COBI may refer to:
People
* Cobi (musician) (Jacob Michael Schmidt, born 1986), an American musician
* Cobi Crispin (born 1988), an Australian wheelchair basketball player
* Cobi Hamilton (born 1990), an American football player
* Cobi Jone ...
then converts this to precorrin-3A:
:precorrin-2 + S-adenosyl methionine
precorrin-3A + S-adenosyl-L-homocysteine
From precorrin-3A to precorrin-3B
Next, the enzyme
CobG transforms precorrin-3A to precorrin-3B:
:precorrin-3A +
NADH
Nicotinamide adenine dinucleotide (NAD) is a coenzyme central to metabolism. Found in all living cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate groups. One nucleotide contains an aden ...
+ H
+ + O
2 precorrin-3B + NAD
+ + H
2O
This enzyme is an
oxidoreductase
In biochemistry, an oxidoreductase is an enzyme that catalyzes the transfer of electrons from one molecule, the reductant, also called the electron donor, to another, the oxidant, also called the electron acceptor. This group of enzymes usually ut ...
that requires oxygen and hence the reaction can only operate under aerobic conditions. The naming of these precorrins as 3A and 3B reflects the fact that each contains three more methyl groups than uroporphyrinogen III but with different structures: in particular, precorrin-3B has an internal
γ-lactone ring formed from the ring A acetic acid sidechain closing back on to the macrocycle.
From precorrin-3B to precorrin-4
The enzyme
CobJ continues the theme of methyl group insertion. Importantly, during this step the
macrocycle
Macrocycles are often described as molecules and ions containing a ring of twelve or more atoms. Classical examples include the crown ethers, calixarenes, porphyrins, and cyclodextrins. Macrocycles describe a large, mature area of chemistry.
...
ring-contracts so that the product contains for the first time the
corrin
Corrin is a heterocyclic compound. It is the parent macrocycle related to the substituted derivative that is found in vitamin B12. Its name reflects that it is the "core" of vitamin B12 (cobalamins).Nelson, D. L.; Cox, M. M. "Lehninger, Princ ...
core which characterises cobalamin.
:
![Precorrin-3B to Precorrin-4](https://upload.wikimedia.org/wikipedia/commons/0/02/Precorrin-3B_to_Precorrin-4.svg)
:precorrin-3B + S-adenosyl methionine
precorrin-4 + S-adenosyl-L-homocysteine
From precorrin-4 to precorrin-5
Methyl group insertions continue as the enzyme
CobM acts on precorrin-4:
:precorrin-4 + S-adenosyl methionine
precorrin-5 + S-adenosyl-L-homocysteine
The newly-inserted methyl group is added to ring C at the carbon attached to the methylene (CH
2) bridge to ring B. This is not its final location on cobalamin as a later step involves its rearrangement to an adjacent ring carbon.
From precorrin-5 to precorrin-6A
The enzyme
CobF now removes the acetyl group located at position 1 of the ring system in precorrin-4 and replaces it with a newly-introduced methyl group. The name of the product, precorrin-6A, reflects the fact that six methyl groups in total have been added to uroporphyrinogen III up to this point. However, since one of these has been extruded with the acetate group, the structure of precorrin-6A contains just the remaining five.
:
![Precorrin-5 to precorrin-6A](https://upload.wikimedia.org/wikipedia/commons/5/5a/Precorrin-5_to_precorrin-6A.svg)
:precorrin-5 + S-adenosyl methionine + H
2O
precorrin-6A + S-adenosyl-L-homocysteine + acetate
From precorrin-6A to precorrin-6B
The enzyme
CobK now
reduces a double bond in ring D using
NADPH
Nicotinamide adenine dinucleotide phosphate, abbreviated NADP or, in older notation, TPN (triphosphopyridine nucleotide), is a cofactor used in anabolic reactions, such as the Calvin cycle and lipid and nucleic acid syntheses, which require NAD ...
:
:precorrin-6A + NADPH + H
+ precorrin-6B + NADP
+
Precorrin-6B therefore differs in structure from precorrin-6A only by having an extra two hydrogen atoms.
From precorrin-6B to precorrin-8
The enzyme
CobL has two active sites, one catalysing two methyl group additions and the other the
decarboxylation
Decarboxylation is a chemical reaction that removes a carboxyl group and releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. The reverse process, which is t ...
of the CH
2COOH group on ring D, so that this substituent becomes a simple methyl group:
:
![Precorrin-6B to precorrin-8](https://upload.wikimedia.org/wikipedia/commons/c/ce/Precorrin-6B_to_precorrin-8.svg)
:precorrin-6B + 2 S-adenosyl methionine
precorrin-8X + 2 S-adenosyl-L-homocysteine + CO
2
From precorrin-8 to hydrogenobyrinic acid
The enzyme
CobH
Cobh ( ,), known from 1849 until 1920 as Queenstown, is a seaport town on the south coast of County Cork, Ireland. With a population of around 13,000 inhabitants, Cobh is on the south side of Great Island in Cork Harbour and home to Ireland's ...
catalyzes a rearrangement reaction, with the result that the methyl group that had been added to ring C is isomerised to its final location, an example of
intramolecular transfer:
:precorrin-8X
hydrogenobyrinate
From hydrogenobyrinic acid to hydrogenobyrinic acid a,c-diamide
The next enzyme in the pathway,
CobB, selectively converts two of the eight carboxylic acid groups into their primary amides.
ATP is used to provide the energy for amide bond formation, with the transferred ammonia coming from
glutamine
Glutamine (symbol Gln or Q) is an α-amino acid that is used in the biosynthesis of proteins. Its side chain is similar to that of glutamic acid, except the carboxylic acid group is replaced by an amide. It is classified as a charge-neutral, ...
:
:hydrogenobyrinic acid + 2 ATP + 2 glutamine + 2 H
2O
hydrogenobyrinic acid a,c-diamide + 2 ADP + 2 phosphate + 2 glutamic acid
From hydrogenobyrinic acid a,c-diamide to acid a,c-diamide
Cobalt(II)
Cobalt is a chemical element with the symbol Co and atomic number 27. As with nickel, cobalt is found in the Earth's crust only in a chemically combined form, save for small deposits found in alloys of natural meteoric iron. The free element, p ...
insertion into the macrocycle is catalysed by the enzyme
Cobalt chelatase
Cobalt chelatase () is an enzyme that catalyzes the chemical reaction
:ATP + hydrogenobyrinic acid a,c-diamide + Co2+ + H2O \rightleftharpoons ADP + phosphate + cob(II)yrinic acid a,c-diamide + H+
The four substrates of this enzyme are ATP, ...
(CobNST):
:hydrogenobyrinic acid a,c-diamide + Co
2+ + ATP + H
2O
acid a,c-diamide + ADP + phosphate + H
+
It is at this stage that the aerobic pathway and the anaerobic pathway merge, with later steps being chemically identical.
Detail of steps from uroporphyrinogen III to a,c-diamide in anaerobic organisms
Many of the steps beyond uroporphyrinogen III in anaerobic organisms such as ''Bacillus megaterium'' involve chemically similar but genetically distinct transformations to those in the aerobic pathway.
From precorrin-2 to cobalt-sirohydrochlorin
The key difference in the pathways is that cobalt is inserted early in anaerobic organisms by first oxidising precorrin-2 to its fully
aromatised form sirohydrochlorin
Sirohydrochlorin is a tetrapyrrole macrocyclic metabolic intermediate in the biosynthesis of sirohaem, the iron-containing prosthetic group in sulfite reductase enzymes. It is also the biosynthetic precursor to cofactor F430, an enzyme which cata ...
and then to that compound's
cobalt(II) complex.
These reactions are catalysed by
CysG and
Sirohydrochlorin cobaltochelatase
The enzyme sirohydrochlorin cobaltochelatase (EC 4.99.1.3) catalyzes the reaction
:cobalt-sirohydrochlorin + 2 H+ = sirohydrochlorin + Co2+
In the forward direction of reactions towards cobalamin in anaerobic bacteria, the two substrates of t ...
.
From cobalt-sirohydrochlorin to cobalt-factor III
As in the aerobic pathway, the third methyl group is introduced by a methyltransferase enzyme,
CbiL:
:cobalt-sirohydrochlorin + S-adenosyl methionine
cobalt-factor III + S-adenosyl-L-homocysteine
From cobalt-factor III to cobalt-precorrin-4
Methylation and ring contraction to form the corrin macrocycle occurs next, catalysed by the enzyme Cobalt-factor III methyltransferase (CbiH, )
:
![Cobalt-precorrin-3 to cobalt-precorrin-4](https://upload.wikimedia.org/wikipedia/commons/5/55/Cobalt-precorrin-3_to_cobalt-precorrin-4.svg)
:cobalt-factor III + S-adenosyl methionine
cobalt-precorrin-4 + S-adenosyl-L-homocysteine
In this pathway, the resulting material contains a δ-lactone, a six-membered ring, rather than the γ-lactone (five-membered ring) of precorrin-3B.
From cobalt-precorrin-4 to cobalt-precorrin-5A
The introduction of the methyl group at C-11 in the next step is catalysed by Cobalt-precorrin-4 methyltransferase (CbiF, )
:cobalt-precorrin-4 + S-adenosyl methionine
cobalt-precorrin-5 + S-adenosyl-L-homocysteine
From cobalt-precorrin-5A to cobalt-precorrin-5B
The scene is now set for the extrusion of the two-carbon fragment corresponding to the acetate released in the formation of precorrin-6A in the aerobic pathway. In this case the fragment released is
acetaldehyde
Acetaldehyde (IUPAC systematic name ethanal) is an organic chemical compound with the formula CH3 CHO, sometimes abbreviated by chemists as MeCHO (Me = methyl). It is a colorless liquid or gas, boiling near room temperature. It is one of the mos ...
and this is catalysed by
CbiG:
: cobalt-precorrin-5A + H
2O
cobalt-precorrin-5B + acetaldehyde + 2 H
+
From cobalt-precorrin-5B to acid a,c-diamide
The steps from cobalt-precorrin-5B to acid a,c-diamide in the anaerobic pathway are essentially chemically identical to those in the aerobic sequence. The intermediates are called cobalt-precorrin-6A, cobalt-precorrin-6B, cobalt-precorrin-8 and cobyrinic acid. The enzymes in sequence are
CbiD;
Cobalt-precorrin-6A reductase (CbiJ, );
CbiT, Cobalt-precorrin-8 methylmutase (CbiC, ) and
CbiA. The final enzyme forms acid a,c-diamide as the two pathways converge.
Detail of steps from acid a,c-diamide to adenosylcobalamin
Aerobic and anaerobic organisms share the same chemical pathway beyond acid a,c-diamide and this is illustrated for the ''cob'' gene products.
From acid a,c-diamide to adenosylcobyric acid
The cobalt(II) is reduced to by the enzyme
CobR
The Cabinet Office Briefing Rooms (COBR) are meeting rooms in the Cabinet Office in London. These rooms are used for committees which co-ordinate the actions of government bodies in response to national or regional crises, or during overseas e ...
and then the enzyme
CobO attaches an adenosyl ligand to the metal. Next, the enzyme
CobQ converts all the carboxylic acids, except the
propionic acid
Propionic acid (, from the Greek words πρῶτος : ''prōtos'', meaning "first", and πίων : ''píōn'', meaning "fat"; also known as propanoic acid) is a naturally occurring carboxylic acid with chemical formula CH3CH2CO2H. It is a liq ...
on ring D, to their primary amides.
From adenosylcobyric acid to adenosylcobinamide phosphate
In aerobic organisms, the enzyme
CobCD now attaches
(R)-1-amino-2-propanol (derived from
threonine
Threonine (symbol Thr or T) is an amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH form under biological conditions), a carboxyl group (which is in the deprotonated −COO ...
) to the propionic acid, forming adenosylcobinamide and the enzyme
CobU phosphorylates
In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, whi ...
the terminal hydroxy group to form adenosylcobinamide phosphate.
The same final product is formed in anaerobic organisms by direct reaction of adenosylcobyric acid with (R)-1-amino-2-propanol O-2-phosphate (derived from threonine-O-phosphate by the enzyme
CobD) catalysed by the enzyme
CbiB.
From adenosylcobinamide phosphate to adenosylcobalamin
In a separate branch of the pathway,
5,6-dimethylbenzimidazole is biosynthesised from
flavin mononucleotide
Flavin mononucleotide (FMN), or riboflavin-5′-phosphate, is a biomolecule produced from riboflavin (vitamin B2) by the enzyme riboflavin kinase and functions as the prosthetic group of various oxidoreductases, including NADH dehydrogenase, as ...
by the enzyme
5,6-dimethylbenzimidazole synthase and converted by
CobT to alpha-ribazole 5' phosphate. Then the enzyme
CobU activates adenosylcobinamide phosphate by formation of adenosylcobinamide-GDP and
CobV links the two substrates to form Adenosylcobalamin-5'-phosphate. In the final step to the coenzyme,
CobC removes the 5' phosphate group:
:Adenosylcobalamin-5'-phosphate + H
2O
adenosylcobalamin + phosphate
The complete biosynthetic route involves a long linear path that requires about 25 contributing enzyme steps.
Other pathways of cobalamin metabolism
Salvage pathways in prokaryotes
Many
prokaryotic species cannot biosynthesize adenosylcobalamin, but can make it from cobalamin. These organisms are capable of cobalamin transport into the cell and its conversion to the required coenzyme form. Even organisms such as ''Salmonella typhimurium'' that can make cobalamin also assimilate it from external sources when available.
Uptake into cells is facilitated by
ABC transporters
The ATP synthase, ATP-binding cassette transporters (ABC transporters) are a transport system superfamily that is one of the largest and possibly one of the oldest gene family, gene families. It is represented in all extant taxon, extant Phylum ...
which absorb the cobalamin through the cell membrane.
Cobalamin metabolism in humans
In humans, dietary sources of cobalamin are bound after ingestion as
transcobalamin
Transcobalamins are carrier proteins which bind cobalamin (B12).
Types
* Transcobalamin I (TCN1), also known as haptocorrin, R-factor, and R-protein, is a glycoprotein produced by the salivary glands of the mouth. It primarily serves to protect ...
s. They are then converted to the coenzyme forms in which they are used.
Methylmalonic aciduria and homocystinuria type C protein is the enzyme which catalyzes the
decyanation of
cyanocobalamin
Cyanocobalamin is a form of vitamin used to treat vitamin deficiency except in the presence of cyanide toxicity. The deficiency may occur in pernicious anemia, following surgical removal of the stomach, with fish tapeworm, or due to bowel ...
as well as the
dealkylation
Alkylation is the transfer of an alkyl group from one molecule to another. The alkyl group may be transferred as an alkyl carbocation, a free radical, a carbanion, or a carbene (or their equivalents). Alkylating agents are reagents for effecting al ...
of alkylcobalamins including methylcobalamin and adenosylcobalamin.
Further reading
*
References
External links
Prof Sir Alan Battersby: the biosynthesis of Vitamin B12St. Catharine's College, Cambridge, video
{{Authority control
Protein families
Vitamin B12
Biosynthesis