Genome Property Definition Page

AccessionGenProp0113
Namecobyrinic acid diamide biosynthesis, aerobic pathway
TypePATHWAY
DescriptionCoenzyme 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 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
Web ReferencesIUBMB: 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 TermGO:0019250: aerobic cobalamin biosynthetic process (biological_process)

Components
Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
C-2, C-7 methylase (CobA)1YESTIGR01469 (HMM): uroporphyrinogen-III C-methyltransferaseGO:0019250: aerobic cobalamin biosynthetic process
hydrogencobyrinate diamide synthase (CobB)10YESTIGR00379 (HMM): cobyrinic acid a,c-diamide synthaseGO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobN subunit11aYESTIGR02257 (HMM): cobaltochelatase, CobN subunitGO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobS subunit11bNOTIGR01651 (HMM): cobaltochelatase, CobT subunitGO:0019250: aerobic cobalamin biosynthetic process
proposed CobX subunit of cobaltochelatase11bc?NOTIGR02442 (HMM): cobaltochelatase subunitGO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobT subunit11cNOTIGR01650 (HMM): cobaltochelatase, CobS subunitGO:0019250: aerobic cobalamin biosynthetic process
CobW cobaltochelatase-associated protein12NOTIGR02475 (HMM): cobalamin biosynthesis protein CobWGO:0019250: aerobic cobalamin biosynthetic process
cobalt reductase (NOT BluB)13YES
C-20 methylase (CobI)2YESTIGR01467 (HMM): precorrin-2 C(20)-methyltransferaseGO:0019250: aerobic cobalamin biosynthetic process
precorrin 3B synthase (CobG/CobZ)3YESTIGR02435 (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)4YESTIGR01466 (HMM): precorrin-3B C17-methyltransferaseGO:0019250: aerobic cobalamin biosynthetic process
C-11 methylase (CobM)5YESTIGR01465 (HMM): precorrin-4 C11-methyltransferaseGO:0019250: aerobic cobalamin biosynthetic process
C1 methylase (CobF)6YESTIGR02434 (HMM): precorrin-6A synthase (deacetylating)GO:0019250: aerobic cobalamin biosynthetic process
precorrin 6 reductase (CobK)7YESTIGR00715 (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)8aYESTIGR02467 (HMM): precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunitGO:0019250: aerobic cobalamin biosynthetic process
CbiT domain, C-5, C-15 methylase/C-12 decarboxylase (CobL)8bYESTIGR02469 (HMM): precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunitGO:0019250: aerobic cobalamin biosynthetic process
C-11, C-12 mutase (CobH)9YESPF02570 (HMM): precorrin-8X methylmutaseGO:0019250: aerobic cobalamin biosynthetic process

Parent Properties
AccessionName
GenProp0274coenzyme B12 biosynthesis - overview


Sibling Properties
AccessionName
GenProp0220uroporhyrinogen III biosynthesis from 5-aminolevulinate
GenProp0269coenzyme B12 biosynthesis from cob(II)yrinate diamide
GenProp0275cobyrinic acid diamide biosynthesis, anaerobic pathway
GenProp0277cobalt import system (ABC transporter: 3.A.1.18.1)