Genome Property Definition Page

Namecobyrinic acid diamide biosynthesis, anaerobic pathway
DescriptionThis 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 PropertyGenProp0274: coenzyme B12 biosynthesis - overview
Literature References
[ 1 ]Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS  Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes.  J Biol Chem 2003 Oct 17;278(42):41148-59. Epub 2003 Jul 17.  PMID 12869542
Gene Ontology TermGO:0019251: anaerobic cobalamin biosynthetic process (biological_process)

Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
cobyrinate diamide synthase (CbiA)CbiAYESTIGR00379 (HMM): cobyrinic acid a,c-diamide synthaseGO:0019251: anaerobic cobalamin biosynthetic process
C-11, C-12 mutase (CbiC)CbiCYESPF02570 (HMM): precorrin-8X methylmutaseGO:0019251: anaerobic cobalamin biosynthetic process
CbiDCbiDYESTIGR00312 (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)CbiEYESTIGR02467 (HMM): precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunitGO:0019251: anaerobic cobalamin biosynthetic process
C-11 methylase (CbiF)CbiFYESTIGR01465 (HMM): precorrin-4 C11-methyltransferaseGO:0019251: anaerobic cobalamin biosynthetic process
CbiGCbiGYESPF01890 (HMM): cobalamin biosynthesis protein, C-terminalGO:0019251: anaerobic cobalamin biosynthetic process
C-17 methylase (CbiH)CbiHYESTIGR01466 (HMM): precorrin-3B C17-methyltransferaseGO:0019251: anaerobic cobalamin biosynthetic process
Co-precorrin 6 reductase (CbiJ)CbiJNOTIGR00715 (HMM): precorrin-6x reductase
PF02571 (HMM): precorrin-6x reductase CbiJ/CobK
GO:0019251: anaerobic cobalamin biosynthetic process
GO:0019251: anaerobic cobalamin biosynthetic process
cobaltochelatase, monomericCbiK/XYESPF06180 (HMM): cobalt chelatase CbiK
PF01903 (HMM): sirohydrochlorin cobaltochelatase
GO:0019251: anaerobic cobalamin biosynthetic process
GO:0019251: anaerobic cobalamin biosynthetic process
C-20 methylase (CbiL)CbiLYESTIGR01467 (HMM): precorrin-2 C(20)-methyltransferaseGO:0019251: anaerobic cobalamin biosynthetic process
C-5,15 methylase/C-12 decarboxylase (CbiT)CbiTYESTIGR02469 (HMM): precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunitGO:0019251: anaerobic cobalamin biosynthetic process
cobalt reductaseCo_redNO
uroporphyrinogen methyltransferase ( (HMM): uroporphyrinogen-III C-methyltransferaseGO:0019251: anaerobic cobalamin biosynthetic process

Parent Properties
GenProp0274coenzyme B12 biosynthesis - overview

Sibling Properties
GenProp0113cobyrinic acid diamide biosynthesis, aerobic pathway
GenProp0220uroporhyrinogen III biosynthesis from 5-aminolevulinate
GenProp0269coenzyme B12 biosynthesis from cob(II)yrinate diamide
GenProp0277cobalt import system (ABC transporter: 3.A.1.18.1)