Genome Property Definition Page
| Accession | GenProp0275 | |
| Name | cobyrinic acid diamide biosynthesis, anaerobic pathway | |
| Type | PATHWAY | |
| Description | This property covers that part of the Vitamin B12 (cobalamin) biosynthesis pathway in which uroporphyrinogen III is converted to cobyrinic acid diamide under anaerobic conditions. This process differs from the aerobic version in several key respects. The most striking is the fact that here the cobalt atom is inserted early in the process (after the formation of the branchpoint compound precorrin-2 by CbiK or CbiX) in an ATP-independent manner, as opposed to the aerobic pathway in which the cobalt is inserted at the end by a multimeric ATP-hydrolyzing system. Another distinctive feature is the nature of the enzyme catalyzing the oxidative ring contraction. In the aerobic pathway, this is carried out by an oxygenase (CobG), while the as-of-yet uncharacterized anaerobic enzyme clearly must utilize some other mechanism. Finally, the methylation at position C-1 at the point of the ring contraction is carried out by CobF in the aerobic pathway, and by an as-of-yet uncharacterized enzyme in the anaerobic pathway (presumably because the proximity of this carbon to the cobalt changes the chemistry somewhat). Two genes (CbiD and CbiG) are found in most anaerobic B12 biosynthetic clusters and have been shown to be essential to the pathway. CbiD is homologous to methylases and is likely to catalyze the C-1 methylation. CbiG then, by process of elimination and (coupled with unique nature of the chemical transformation) its lack of homology to other known classes of enzyme is likely to catalyze the ring contraction. CbiJ, the analog of precorrin-6x reductase (CobK), is not found in deltaproteobacteria, a number of archaea and a scattering of other species, oftentimes this is the only component missing. Most likely, an unknown reductase replaces CbiJ/CobK in these species. For this reason, the detection of this component is not a requirement for the assertion of YES for this property. The majority of genomes for which some evidence has been asserted are missing evidence of the CbiK or CbiX chelatase. This step is still required for assertion of the YES state since it is part of the suite of components which are diagnostic for the anaerobic pathway. The evidence for the anaerobic pathway is nonetheless quite strong when this is the only component missing, especially when the aerobic pathway is not supported. | |
| Parent Property | GenProp0274: coenzyme B12 biosynthesis - overview | |
| Literature References |
| |
| Gene Ontology Term | GO:0019251: anaerobic cobalamin biosynthetic process (biological_process) |
Components
| Step Name | Step Num | Required | Evidence (Method) | Evidence Go Terms |
|---|---|---|---|---|
| cobyrinate diamide synthase (CbiA) | CbiA | YES | TIGR00379 (HMM): cobyrinic acid a,c-diamide synthase | GO:0019251: anaerobic cobalamin biosynthetic process |
| C-11, C-12 mutase (CbiC) | CbiC | YES | PF02570 (HMM): precorrin-8X methylmutase | GO:0019251: anaerobic cobalamin biosynthetic process |
| CbiD | CbiD | YES | TIGR00312 (HMM): cobalamin biosynthesis protein CbiD PF01888 (HMM): CbiD | GO:0019251: anaerobic cobalamin biosynthetic process GO:0019251: anaerobic cobalamin biosynthetic process |
| C-5,15 methylase/C-12 decarboxylase (CbiE) | CbiE | YES | TIGR02467 (HMM): precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit | GO:0019251: anaerobic cobalamin biosynthetic process |
| C-11 methylase (CbiF) | CbiF | YES | TIGR01465 (HMM): precorrin-4 C11-methyltransferase | GO:0019251: anaerobic cobalamin biosynthetic process |
| CbiG | CbiG | YES | PF01890 (HMM): cobalamin biosynthesis protein, C-terminal | GO:0019251: anaerobic cobalamin biosynthetic process |
| C-17 methylase (CbiH) | CbiH | YES | TIGR01466 (HMM): precorrin-3B C17-methyltransferase | GO:0019251: anaerobic cobalamin biosynthetic process |
| Co-precorrin 6 reductase (CbiJ) | CbiJ | NO | TIGR00715 (HMM): precorrin-6x reductase PF02571 (HMM): precorrin-6x reductase CbiJ/CobK | GO:0019251: anaerobic cobalamin biosynthetic process GO:0019251: anaerobic cobalamin biosynthetic process |
| cobaltochelatase, monomeric | CbiK/X | YES | PF06180 (HMM): cobalt chelatase CbiK PF01903 (HMM): sirohydrochlorin cobaltochelatase | GO:0019251: anaerobic cobalamin biosynthetic process GO:0019251: anaerobic cobalamin biosynthetic process |
| C-20 methylase (CbiL) | CbiL | YES | TIGR01467 (HMM): precorrin-2 C(20)-methyltransferase | GO:0019251: anaerobic cobalamin biosynthetic process |
| C-5,15 methylase/C-12 decarboxylase (CbiT) | CbiT | YES | TIGR02469 (HMM): precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit | GO:0019251: anaerobic cobalamin biosynthetic process |
| cobalt reductase | Co_red | NO | ||
| uroporphyrinogen methyltransferase (2.1.1.107) | CobA | YES | TIGR01469 (HMM): uroporphyrinogen-III C-methyltransferase | GO:0019251: anaerobic cobalamin biosynthetic process |
Parent Properties
| Accession | Name |
|---|---|
| GenProp0274 | coenzyme B12 biosynthesis - overview |
Sibling Properties
| Accession | Name |
|---|---|
| GenProp0113 | cobyrinic acid diamide biosynthesis, aerobic pathway |
| GenProp0220 | uroporhyrinogen III biosynthesis from 5-aminolevulinate |
| GenProp0269 | coenzyme B12 biosynthesis from cob(II)yrinate diamide |
| GenProp0277 | cobalt import system (ABC transporter: 3.A.1.18.1) |