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MetaCyc Pathway: adenosylcobalamin biosynthesis I (early cobalt insertion)

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Synonyms: anaerobic adenosylcobalamin biosynthesis, vitamin B12 biosynthesis

Superclasses: Biosynthesis Cofactors, Prosthetic Groups, Electron Carriers Biosynthesis Vitamins Biosynthesis Cobalamin Biosynthesis Adenosylcobalamin Biosynthesis
Superpathways

Some taxa known to possess this pathway include ? : Bacillus megaterium , Chlorobaculum tepidum , Leptospira interrogans , Methanocaldococcus jannaschii , Methanothermobacter thermautotrophicus , Propionibacterium freudenreichii , Propionibacterium freudenreichii shermanii , Salmonella enterica enterica serovar Typhimurium

Expected Taxonomic Range: Archaea , Bacteria

Summary:
General Background

Vitamin B12 (also known as adenosylcobalamin 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 [Warren02].

Vitamin B12 is one of the most structurally complex small molecules made in Nature. It contains a contracted porphinoid ring with a cobalt ion ligated at its center and further held in place by a lower axial base (a dimethylbenzimidazole) and an upper methyl or adenosyl group. Its biosynthesis is similarly complex, and requires more than thirty genes. It's biosynthesis is confined to only some bacteria and archaea [Martens02].

Two main pathways are known for coenzyme B12 biosynthesis - an aerobic pathway (see adenosylcobalamin biosynthesis II (late cobalt incorporation)) and an anaerobic pathway (this pathway). 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 latter part of the pathway is identical, or at least very similar.

About This Pathway

The best characterized anaerobic pathway is the one from Salmonella enterica enterica serovar Typhimurium, although much of the early work was performed with the bacterium Propionibacterium freudenreichii shermanii and much of the more recent work was done with the bacterium Bacillus megaterium.

The biosynthesis of coenzyme B12 starts with the biosynthesis of the tetrapyrrole intermediate uroporphyrinogen-III, 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, eliminating carbon C-20 from the ring. This contraction process converts the ring from a porphyrin ring to a corrin ring. Both the C-20 carbon and the added C-20 methyl group are lost in the form of acetaldehyde.

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.

There is indeed some uncertainty about the path from precorrin-2 to cobalt-precorrin-3. Early work, performed mostly with Salmonella enterica, suggested that this transition may be catalyzed in two steps - the insertion of cobalt into precorrin-2, which is catalyzed by cbiK, followed by methylation by cbiL. However, information gathered from multiple studies, most recently with the aerobic bacterium Bacillus megaterium that posseses a complete anaerobic pathway, suggests that this conversion may proceed through the oxidized factor intermediates, which is favored for the ease of cobalt insertion. Thus, precorrin-2 is first oxidized to sirohydrochlorin by cysG. Cobalt in then inserted (either by cbiK or cbiX), followed by methylation to cobalt-factor III and reduction to cobalt-precorrin-3 [Raux03, Frank07a, Frank05, Leech03, Brindley03, Moore13].

The first intermediate with a corrin ring is cobyrinate. However, this intermediate still needs to be modified extensively. Successive amidation reactions transfer amide groups from two L-glutamine molecules to the carboxy groups a and c, resulting in cob(II)yrinate a,c-diamide. The Co2+ ion is then reduced to Co1+, and the molecule is adenosylated to form adenosyl-cobyrinate a,c-diamide. Additional amidation of the carboxyl 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 at aminopropanol phosphate biosynthesis I and 5,6-dimethylbenzimidazole biosynthesis.

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. Recent findings suggest that (R)-1-amino-2-propanol O-2-phosphate is formed and added to adenosylcobyrate, forming |adenosyl-cobinamide phosphate, which is then phosphorylated by GTP to form adenosylcobinamide-GDP.

At least in Salmonella enterica enterica serovar Typhimurium α-ribazole 5'-phosphate, which is formed from 5,6-dimethylbenzimidazole, is then added, forming adenosylcobalamin 5'-phosphate [Zayas07]. The last reaction in the pathway is the dephosphorylation of adenosylcobalamin 5'-phosphate to coenzyme B12.

coenzyme B12 biosynthesis in archaea

It is well documented that some archaebacteria synthesize and require cobamides to live. For example, methanogens contain extraordinarily high concentrations of cobamides, in the form of cobalt-factor III and Pseudo B12, which are required for methanogenesis from H2, CO2, acetate and methanol [Buan06, Yin06, Hagemeier06] (for a review see [DiMarco90]). Other archaea, such as the halophile Halobacterium sp. NRC-1 [Woodson03], the sulfur metabolizing Acidianus ambivalens [Krautler88] and the thermophile Moorella thermoacetica [Das07] also require cobamides. Comparative genomics studies find cobalamin biosynthetic genes in many archaea [Rodionov03]. However, at this point the actual pathways employed by archaebacteria are not well understood.

Subpathways: cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion) , adenosylcobalamin biosynthesis from cobyrinate a,c-diamide I , tetrapyrrole biosynthesis I (from glutamate) , aminopropanol phosphate biosynthesis I , 5,6-dimethylbenzimidazole biosynthesis

Variants: adenosylcobalamin biosynthesis II (late cobalt incorporation) , adenosylcobalamin salvage from cobalamin , adenosylcobalamin salvage from cobinamide I , adenosylcobalamin salvage from cobinamide II

Credits:
Created 20-Apr-2007 by Caspi R , SRI International
Revised 21-Feb-2013 by Caspi R , SRI International
Revised 25-Sep-2013 by Caspi R , SRI International


References

Brindley03: Brindley AA, Raux E, Leech HK, Schubert HL, Warren MJ (2003). "A story of chelatase evolution: identification and characterization of a small 13-15-kDa "ancestral" cobaltochelatase (CbiXS) in the archaea." J Biol Chem 278(25);22388-95. PMID: 12686546

Buan06: Buan NR, Rehfeld K, Escalante-Semerena JC (2006). "Studies of the CobA-type ATP:Co(I)rrinoid adenosyltransferase enzyme of Methanosarcina mazei strain Go1." J Bacteriol 188(10);3543-50. PMID: 16672609

Das07: Das A, Fu ZQ, Tempel W, Liu ZJ, Chang J, Chen L, Lee D, Zhou W, Xu H, Shaw N, Rose JP, Ljungdahl LG, Wang BC (2007). "Characterization of a corrinoid protein involved in the C1 metabolism of strict anaerobic bacterium Moorella thermoacetica." Proteins 67(1);167-76. PMID: 17211893

DiMarco90: DiMarco AA, Bobik TA, Wolfe RS (1990). "Unusual coenzymes of methanogenesis." Annu Rev Biochem 59;355-94. PMID: 2115763

Frank05: Frank S, Brindley AA, Deery E, Heathcote P, Lawrence AD, Leech HK, Pickersgill RW, Warren MJ (2005). "Anaerobic synthesis of vitamin B12: characterization of the early steps in the pathway." Biochem Soc Trans 33(Pt 4);811-4. PMID: 16042604

Frank07a: Frank S, Deery E, Brindley AA, Leech HK, Lawrence AD, Heathcote P, Schubert HL, Brocklehurst K, Rigby SE, Warren MJ, Pickersgill RW (2007). "Elucidation of substrate specificity in the cobalamin (vitamin B12) biosynthetic methyltransferases; structure and function of the C20 methyltransferase (CbiL) from Methanothermobacter thermautotrophicus." J Biol Chem. PMID: 17567575

Hagemeier06: Hagemeier CH, Krer M, Thauer RK, Warkentin E, Ermler U (2006). "Insight into the mechanism of biological methanol activation based on the crystal structure of the methanol-cobalamin methyltransferase complex." Proc Natl Acad Sci U S A 103(50);18917-22. PMID: 17142327

Krautler88: Krautler B, Kohler HP, Stupperich E (1988). "5'-Methylbenzimidazolyl-cobamides are the corrinoids from some sulfate-reducing and sulfur-metabolizing bacteria." Eur J Biochem 176(2);461-9. PMID: 3416881

Leech03: Leech HK, Raux E, McLean KJ, Munro AW, Robinson NJ, Borrelly GP, Malten M, Jahn D, Rigby SE, Heathcote P, Warren MJ (2003). "Characterization of the cobaltochelatase CbiXL: evidence for a 4Fe-4S center housed within an MXCXXC motif." J Biol Chem 278(43);41900-7. PMID: 12917443

Martens02: Martens JH, Barg H, Warren MJ, Jahn D (2002). "Microbial production of vitamin B12." Appl Microbiol Biotechnol 58(3);275-85. PMID: 11935176

Minot26: Minot, G.R., Murphy, W.P. (1926). "Treatment of pernicious anaemia by a special diet." J. Am. Med. Assoc. 87:470-476.

Moore13: Moore SJ, Biedendieck R, Lawrence AD, Deery E, Howard MJ, Rigby SE, Warren MJ (2013). "Characterization of the enzyme CbiH60 involved in anaerobic ring contraction of the cobalamin (vitamin B12) biosynthetic pathway." J Biol Chem 288(1);297-305. PMID: 23155054

Rasetti81: Rasetti V, Pfaltz A, Kratky C, Eschenmoser A (1981). "Ring contraction of hydroporphinoid to corrinoid complexes." Proc Natl Acad Sci U S A 78(1);16-19. PMID: 16592942

Raux03: Raux E, Leech HK, Beck R, Schubert HL, Santander PJ, Roessner CA, Scott AI, Martens JH, Jahn D, Thermes C, Rambach A, Warren MJ (2003). "Identification and functional analysis of enzymes required for precorrin-2 dehydrogenation and metal ion insertion in the biosynthesis of sirohaem and cobalamin in Bacillus megaterium." Biochem J 370(Pt 2);505-16. PMID: 12408752

Rickes48: Rickes, E. L., Brink, N. G., Koniuszy, F. R., Wood, T. R., Folkers, K. (1948). "Crystalline vitamin B12." Science 107: 396-397.

Rodionov03: Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS (2003). "Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes." J Biol Chem 278(42);41148-59. PMID: 12869542

Roessner06: Roessner CA, Scott AI (2006). "Fine-tuning our knowledge of the anaerobic route to cobalamin (vitamin B12)." J Bacteriol 188(21);7331-4. PMID: 16936030

Smith48: Smith, E. L. (1948). "Purification of antipernicious anemia factors from liver." Nature 161: 638-639.

Warren02: Warren MJ, Raux E, Schubert HL, Escalante-Semerena JC (2002). "The biosynthesis of adenosylcobalamin (vitamin B12)." Nat Prod Rep 19(4);390-412. PMID: 12195810

Woodson03: Woodson JD, Peck RF, Krebs MP, Escalante-Semerena JC (2003). "The cobY gene of the archaeon Halobacterium sp. strain NRC-1 is required for de novo cobamide synthesis." J Bacteriol 185(1);311-6. PMID: 12486068

Yin06: Yin J, Xu LX, Cherney MM, Raux-Deery E, Bindley AA, Savchenko A, Walker JR, Cuff ME, Warren MJ, James MN (2006). "Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus." J Struct Funct Genomics 7(1);37-50. PMID: 16835730

Zayas07: Zayas CL, Escalante-Semerena JC (2007). "Reassessment of the late steps of coenzyme B12 synthesis in Salmonella enterica: evidence that dephosphorylation of adenosylcobalamin-5'-phosphate by the CobC phosphatase is the last step of the pathway." J Bacteriol 189(6);2210-8. PMID: 17209023

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Alwan89: Alwan AF, Mgbeje BI, Jordan PM (1989). "Purification and properties of uroporphyrinogen III synthase (co-synthase) from an overproducing recombinant strain of Escherichia coli K-12." Biochem J 264(2);397-402. PMID: 2557837

Anderson79: Anderson PM, Desnick RJ (1979). "Purification and properties of delta-aminolevulinate dehydrase from human erythrocytes." J Biol Chem 254(15);6924-30. PMID: 457661

Balg07: Balg C, Blais SP, Bernier S, Huot JL, Couture M, Lapointe J, Chenevert R (2007). "Synthesis of beta-ketophosphonate analogs of glutamyl and glutaminyl adenylate, and selective inhibition of the corresponding bacterial aminoacyl-tRNA synthetases." Bioorg Med Chem 15(1);295-304. PMID: 17049867

Battersby80: Battersby AR, Fookes CJ, Matcham GW, McDonald E (1980). "Biosynthesis of the pigments of life: formation of the macrocycle." Nature 285(5759);17-21. PMID: 6769048

Bernier05: Bernier S, Dubois DY, Habegger-Polomat C, Gagnon LP, Lapointe J, Chenevert R (2005). "Glutamylsulfamoyladenosine and pyroglutamylsulfamoyladenosine are competitive inhibitors of E. coli glutamyl-tRNA synthetase." J Enzyme Inhib Med Chem 20(1);61-7. PMID: 15895686

Blanche89: Blanche F, Debussche L, Thibaut D, Crouzet J, Cameron B (1989). "Purification and characterization of S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase from Pseudomonas denitrificans." J Bacteriol 171(8);4222-31. PMID: 2546914

Blanche91: Blanche F, Debussche L, Famechon A, Thibaut D, Cameron B, Crouzet J (1991). "A bifunctional protein from Pseudomonas denitrificans carries cobinamide kinase and cobinamide phosphate guanylyltransferase activities." J Bacteriol 1991;173(19);6052-7. PMID: 1655696

Blanche91a: Blanche F, Robin C, Couder M, Faucher D, Cauchois L, Cameron B, Crouzet J (1991). "Purification, characterization, and molecular cloning of S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase from Methanobacterium ivanovii." J Bacteriol 173(15);4637-45. PMID: 1856165

Blanche91b: Blanche F, Couder M, Debussche L, Thibaut D, Cameron B, Crouzet J (1991). "Biosynthesis of vitamin B12: stepwise amidation of carboxyl groups b, d, e, and g of cobyrinic acid a,c-diamide is catalyzed by one enzyme in Pseudomonas denitrificans." J Bacteriol 1991;173(19);6046-51. PMID: 1917839

Blanche92: Blanche F, Maton L, Debussche L, Thibaut D (1992). "Purification and characterization of Cob(II)yrinic acid a,c-diamide reductase from Pseudomonas denitrificans." J Bacteriol 1992;174(22);7452-4. PMID: 1429467

Blanche95: Blanche F., Cameron B., Crouzet J., Debussche L., Thibaut D., Vuilhorgne M., Leeper F. J., Battersby A. R. (1995). "Vitamin B12: how the problem of its biosynthesis was solved." Angewandte Chemie. International edition in English 34(4): 383-411.

Bollivar04: Bollivar DW, Clauson C, Lighthall R, Forbes S, Kokona B, Fairman R, Kundrat L, Jaffe EK (2004). "Rhodobacter capsulatus porphobilinogen synthase, a high activity metal ion independent hexamer." BMC Biochem 5;17. PMID: 15555082

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Brushaber98: Brushaber KR, O'Toole GA, Escalante-Semerena JC (1998). "CobD, a novel enzyme with L-threonine-O-3-phosphate decarboxylase activity, is responsible for the synthesis of (R)-1-amino-2-propanol O-2-phosphate, a proposed new intermediate in cobalamin biosynthesis in Salmonella typhimurium LT2." J Biol Chem 273(5);2684-91. PMID: 9446573

Cameron91: Cameron B, Blanche F, Rouyez MC, Bisch D, Famechon A, Couder M, Cauchois L, Thibaut D, Debussche L, Crouzet J (1991). "Genetic analysis, nucleotide sequence, and products of two Pseudomonas denitrificans cob genes encoding nicotinate-nucleotide: dimethylbenzimidazole phosphoribosyltransferase and cobalamin (5'-phosphate) synthase." J Bacteriol 1991;173(19);6066-73. PMID: 1917841

Campbell06: Campbell GR, Taga ME, Mistry K, Lloret J, Anderson PJ, Roth JR, Walker GC (2006). "Sinorhizobium meliloti bluB is necessary for production of 5,6-dimethylbenzimidazole, the lower ligand of B12." Proc Natl Acad Sci U S A 103(12);4634-9. PMID: 16537439

Campbell73: Campbell RL, Dekker EE (1973). "Formation of D-1-amino-2-propanol from L-threonine by enzymes from Escherichia coli K-12." Biochem Biophys Res Commun 53(2);432-8. PMID: 4577583

Campbell78: Campbell RL, Swain RR, Dekker EE (1978). "Purification, separation, and characterization of two molecular forms of D-1-amino-2-propanol:NAD+ oxidoreductase activity from extracts of Escherichia coli K-12." J Biol Chem 253(20);7282-8. PMID: 359547

Cantoni84: Cantoni L, Dal Fiume D, Ruggieri R (1984). "Decarboxylation of uroporphyrinogen I and III in 2,3,7,8-tetrachlorodibenzo-p-dioxin induced porphyria in mice." Int J Biochem 16(5);561-5. PMID: 6724109

Chen95: Chen P, Ailion M, Weyand N, Roth J (1995). "The end of the cob operon: evidence that the last gene (cobT) catalyzes synthesis of the lower ligand of vitamin B12, dimethylbenzimidazole." J Bacteriol 177(6);1461-9. PMID: 7883701

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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