If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.
Synonyms: adenosylcobalamin biosynthesis II (late cobalt incorporation), vitamin B12 biosynthesis
|Superclasses:||Biosynthesis → Cofactors, Prosthetic Groups, Electron Carriers Biosynthesis → Vitamins Biosynthesis → Cobalamin Biosynthesis → Adenosylcobalamin Biosynthesis → De Novo Adenosylcobalamin Biosynthesis|
Adenosylcobalamin (also known as vitamin B12 or coenzyme B12) was discovered in the 1920s after Minot and Murphy reported that they could cure the symptoms of pernicious anaemia by feeding patients with crude liver extract [Minot26] (they received the Nobel prize in 1934 for this discovery). The unknown factor has been isolated and subsequently crystallized in 1948 [Smith48, Rickes48], and was given the name vitamin B12 and, as it was shown to contain a cobalt ion, cobalamin (although this term is used to describe a family of related compounds) [Warren02].
Cobalamins are some of the most structurally complex small molecules made in Nature. They contain a contracted porphinoid ring with a cobalt ion ligated at its center and further held in place by a lower axial base ( 5,6-dimethylbenzimidazole) and a methyl or adenosyl group that function as an upper axial ligand. Their biosynthesis is similarly complex, and requires more than thirty genes. Cobalamin biosynthesis is confined to only some bacteria and archaea [Martens02].
Two main pathways are known for adenosylcobalamin biosynthesis - an aerobic pathway (this pathway) and an anaerobic pathway (see adenosylcobalamin biosynthesis I (anaerobic)). The main differences between these pathways are the timing of the Co2+ ion insertion and the ring-contraction mechanism (for more about ring contraction, see [Rasetti81]). Co2+ is inserted early on in the anaerobic pathway, and rather late in the aerobic pathway. The two different routes then merge at cob(II)yrinate a,c-diamide, and the later part of the pathway is identical, or at least very similar.
About This Pathway
The biosynthesis of adenosylcobalamin starts with the biosynthesis of the tetrapyrrole intermediate uroporphyrinogen-III, which is a common intermediate in the biosynthesis of several important compounds, such as heme and chlorophyl. Uroporphyrinogen III is converted to a corrin ring by a complex process that involves (among other things) the attachment of eight methyl groups, all derived from S-adenosyl-L-methionine (SAM). During the process the ring contracts via bonding of carbons C-1 and C-19 to each other, eliminating carbon C-20 from the ring. Both the C-20 carbon and the added C-20 methyl group are lost in the form of acetate.
The intermediates formed prior to the formation of the corrin ring are called precorrins. The precorrins are numbered corresponding to the number of methyl groups that have been already introduced. If two different intermediates have the same number of methyl groups, they are also labeled by A or B (as in precorrin-6A). If there is still some uncertainty about an intermediate, it is given a temporary designation of X or Y.
The first committed step in this pathway is the addition of a methyl group to carbon C-20 of the tetrapyrrole ring to give precorrin-3A. This intermediate, which contains three additional methyl groups (compared with uroporphyrinogen-III), is oxidized by precorrin-3B synthase, using molecular oxygen, to precorrin-3B, an intermediate that has been described as "spring-loaded for contraction" [Warren02]. This intermediate, which has a hydroxy group at carbon C-20, forms a lactone between carbons C-1 and C-2. However, the ring is not contracted until the next enzyme (another methyltransferase) adds a methyl group to carbon C-17. At this point the ring contracts, forming the next intermediate, precorrin-4. Following the addition of four more methyl groups (at positions C-11, C-1, C-5 and C-15) and the release of acetate and CO2, the final precorrin intermediate, precorrin-8x, is formed. This intermediate is the substrate for the enzyme precorrin-8x methylmutase subunit, which finally converts it to a true corrin ring compound, hydrogenobyrinate.
This corrin ring intermediate still requires an extensive modification. Successive amidation reactions transfer two amide groups from two L-glutamine molecules to the carboxy groups a and c, resulting in cob(II)yrinate a,c-diamide, and a Co2+ ion is inserted into the ring by the enzyme cobaltochelatase, forming cob(II)yrinate a,c-diamide - the point where the early-insertion and late-insertion pathways combine.
The Co2+ ion is immediately reduced to Co1+ and is adenosylated to form adenosyl-cobyrinate a,c-diamide. Additional amidation of carboxy groups b, d, e and g generates adenosylcobyrate. At this point the lower ligand base is synthesized and tethered to the corrin ring via a structure known as the nucleotide loop, which is composed of some form of (R)-1-aminopropan-2-ol and 5,6-dimethylbenzimidazole. More information about the biosynthesis of these side chains is provided in the pathways aminopropanol phosphate biosynthesis I and 5,6-dimethylbenzimidazole biosynthesis I (aerobic).
There is some uncertainty about the order in which some of the final reactions of the pathway occur. Depending on the order of the reactions, different intermediates may form. It was initially assumed that (R)-1-aminopropan-2-ol serves as substrate for the enzyme that attaches it to adenosylcobyrate. However, the Km value for (R)-1-aminopropan-2-ol is very high (20mM), suggesting this may not be the natural substrate. Recent findings in Salmonella enterica enterica serovar Typhimurium suggest that the natural substrate is actually (R)-1-amino-2-propanol O-2-phosphate. In this case the product of the reaction is adenosyl-cobinamide phosphate, which is further phosphorylated by GTP to adenosylcobinamide-GDP [Brushaber98]. Even though this has not been proven in Pseudomonas denitrificans, we have decided to present the pathway using this route. Another uncertainty concerns the addition of α-ribazole 5'-phosphate to adenosylcobinamide-GDP. The adenosyl-cobalamin (5'-phosphate) synthase enzyme isolated from Pseudomonas denitrificans accepts both α-ribazole and α-ribazole 5'-phosphate as substrates [Cameron91]. It is not clear whether α-ribazole 5'-phosphate is added directly, generating adenosylcobalamin 5'-phosphate, followed by dephosphorylation to adenosylcobalamin (as shown here), or whether the phosphate group is first removed from α-ribazole 5'-phosphate, in which case α-ribazole is added, and the product is adenosylcobalamin. We have chosen to use the first option in this pathway diagram.
Subpathways: adenosylcobalamin biosynthesis from cobyrinate a,c-diamide I, cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation), tetrapyrrole biosynthesis I (from glutamate), aminopropanol phosphate biosynthesis I, 5,6-dimethylbenzimidazole biosynthesis I (aerobic)
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