Genome Property Definition Page
Accession | GenProp0113 | |
Name | cobyrinic acid diamide biosynthesis, aerobic pathway | |
Type | PATHWAY | |
Description | Coenzyme B12 (5-Deoxyadenosyl cobalamin) is biosynthesized in prokaryotes via a complex pathway from uroporphyrinogen III (an intermediate in the biosynthesis of heme) and S-adenosylmethionine, glutamine, cobalt, glycine, acetyl-CoA, beta-nicotinate mononucleotide and dimethylbenzimidazole. This property is the first section, from uroporphyrinogen III to just after colbalt insertion. This version of the pathway includes an oxygen-requiring enzyme (CobG) and differs from the anaerobic pathway in which the cobalt is inserted early in the process by an ATP-independent chelatase (CbiK or CbiX). The other distinctive feature of the aerobic pathway is the C-1 methylase (CobF) which is replaced by the non-homologous CbiD in the anaerobic process. The cobalt(II) reductase (BluB) which constitutes the final step of this property is also distinctive for the aerobic path, although the anaerobic enzyme(s) have not been well studied. The well-characterized trimeric ATP-dependent cobaltochelatase (CobNST) is completely detected only in a narrow range of prokaryotes. In a number of other species which appear to otherwise utilize the aerobic pathway, CobST is apparently replaced with another subunit repated to magnesium chelatases which we tentatively refer to here as CobX. For this reason, only the CobN subunit is relied upon here for the assertion of the YES state. Many species exhibit ony one or two of the components distinctive of the aerobic pathway (and are either aerobes, microaerophiles or facultative anaerobes), possibly indicating non-homologous families as-of-yet uncharacterized. | |
Parent Property | GenProp0274: coenzyme B12 biosynthesis - overview | |
Literature References |
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Web References | IUBMB: Corrin Biosynthesis (part 1) IUBMB: Corrin and Siroheme Biosynthesis (part 2) IUBMB: Corrin Biosynthesis (part 3) IUBMB: Corrin Biosynthesis (anaerobic) IUBMB: Corrin Biosynthesis (part 4) IUBMB: Corrin Biosynthesis (part 5) IUBMB: Corrin Biosynthesis (part 6) IUBMB: Corrin Biosynthesis (part 7) IUBMB: Corrin Biosynthesis (part 8) | |
Gene Ontology Term | GO:0019250: aerobic cobalamin biosynthetic process (biological_process) |
Components
Step Name | Step Num | Required | Evidence (Method) | Evidence Go Terms |
---|---|---|---|---|
C-2, C-7 methylase (CobA) | 1 | YES | TIGR01469 (HMM): uroporphyrinogen-III C-methyltransferase | GO:0019250: aerobic cobalamin biosynthetic process |
hydrogencobyrinate diamide synthase (CobB) | 10 | YES | TIGR00379 (HMM): cobyrinic acid a,c-diamide synthase | GO:0019250: aerobic cobalamin biosynthetic process |
cobaltochelatase, CobN subunit | 11a | YES | TIGR02257 (HMM): cobaltochelatase, CobN subunit | GO:0019250: aerobic cobalamin biosynthetic process |
cobaltochelatase, CobS subunit | 11b | NO | TIGR01651 (HMM): cobaltochelatase, CobT subunit | GO:0019250: aerobic cobalamin biosynthetic process |
proposed CobX subunit of cobaltochelatase | 11bc? | NO | TIGR02442 (HMM): cobaltochelatase subunit | GO:0019250: aerobic cobalamin biosynthetic process |
cobaltochelatase, CobT subunit | 11c | NO | TIGR01650 (HMM): cobaltochelatase, CobS subunit | GO:0019250: aerobic cobalamin biosynthetic process |
CobW cobaltochelatase-associated protein | 12 | NO | TIGR02475 (HMM): cobalamin biosynthesis protein CobW | GO:0019250: aerobic cobalamin biosynthetic process |
cobalt reductase (NOT BluB) | 13 | YES | ||
C-20 methylase (CobI) | 2 | YES | TIGR01467 (HMM): precorrin-2 C(20)-methyltransferase | GO:0019250: aerobic cobalamin biosynthetic process |
precorrin 3B synthase (CobG/CobZ) | 3 | YES | TIGR02435 (HMM): precorrin-3B synthase TIGR02485 (HMM): precorrin 3B synthase CobZ | GO:0019250: aerobic cobalamin biosynthetic process GO:0019250: aerobic cobalamin biosynthetic process |
C-17 methylase (CobJ) | 4 | YES | TIGR01466 (HMM): precorrin-3B C17-methyltransferase | GO:0019250: aerobic cobalamin biosynthetic process |
C-11 methylase (CobM) | 5 | YES | TIGR01465 (HMM): precorrin-4 C11-methyltransferase | GO:0019250: aerobic cobalamin biosynthetic process |
C1 methylase (CobF) | 6 | YES | TIGR02434 (HMM): precorrin-6A synthase (deacetylating) | GO:0019250: aerobic cobalamin biosynthetic process |
precorrin 6 reductase (CobK) | 7 | YES | TIGR00715 (HMM): precorrin-6x reductase PF02571 (HMM): precorrin-6x reductase CbiJ/CobK | GO:0019250: aerobic cobalamin biosynthetic process GO:0019250: aerobic cobalamin biosynthetic process |
CbiE domain, C-5, C-15 methylase/C-12 decarboxylase (CobL) | 8a | YES | TIGR02467 (HMM): precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit | GO:0019250: aerobic cobalamin biosynthetic process |
CbiT domain, C-5, C-15 methylase/C-12 decarboxylase (CobL) | 8b | YES | TIGR02469 (HMM): precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit | GO:0019250: aerobic cobalamin biosynthetic process |
C-11, C-12 mutase (CobH) | 9 | YES | PF02570 (HMM): precorrin-8X methylmutase | GO:0019250: aerobic cobalamin biosynthetic process |
Parent Properties
Accession | Name |
---|---|
GenProp0274 | coenzyme B12 biosynthesis - overview |
Sibling Properties
Accession | Name |
---|---|
GenProp0220 | uroporhyrinogen III biosynthesis from 5-aminolevulinate |
GenProp0269 | coenzyme B12 biosynthesis from cob(II)yrinate diamide |
GenProp0275 | cobyrinic acid diamide biosynthesis, anaerobic pathway |
GenProp0277 | cobalt import system (ABC transporter: 3.A.1.18.1) |