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
GenProp0274: coenzyme B12 biosynthesis - overview
GenProp0274: 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
[ 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
[ 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)
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)
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 TermGO:0019250: aerobic cobalamin biosynthetic process (biological_process)
GO:0019250: aerobic cobalamin biosynthetic process (biological_process)
GO:0019250: aerobic cobalamin biosynthetic process (biological_process)
GO:0019250: aerobic cobalamin biosynthetic process (biological_process)
GO:0019250: aerobic cobalamin biosynthetic process (biological_process)
GO:0019250: aerobic cobalamin biosynthetic process (biological_process)
GO:0019250: aerobic cobalamin biosynthetic process (biological_process)
GO:0019250: aerobic cobalamin biosynthetic process (biological_process)
GO: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-methyltransferase
TIGR01469 (HMM): uroporphyrinogen-III C-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-2, C-7 methylase (CobA)1YESTIGR01469 (HMM): uroporphyrinogen-III C-methyltransferase
TIGR01469 (HMM): uroporphyrinogen-III C-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-2, C-7 methylase (CobA)1YESTIGR01469 (HMM): uroporphyrinogen-III C-methyltransferase
TIGR01469 (HMM): uroporphyrinogen-III C-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
hydrogencobyrinate diamide synthase (CobB)10YESTIGR00379 (HMM): cobyrinic acid a,c-diamide synthase
TIGR00379 (HMM): cobyrinic acid a,c-diamide synthase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
hydrogencobyrinate diamide synthase (CobB)10YESTIGR00379 (HMM): cobyrinic acid a,c-diamide synthase
TIGR00379 (HMM): cobyrinic acid a,c-diamide synthase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
hydrogencobyrinate diamide synthase (CobB)10YESTIGR00379 (HMM): cobyrinic acid a,c-diamide synthase
TIGR00379 (HMM): cobyrinic acid a,c-diamide synthase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobN subunit11aYESTIGR02257 (HMM): cobaltochelatase, CobN subunit
TIGR02257 (HMM): cobaltochelatase, CobN subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobN subunit11aYESTIGR02257 (HMM): cobaltochelatase, CobN subunit
TIGR02257 (HMM): cobaltochelatase, CobN subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobN subunit11aYESTIGR02257 (HMM): cobaltochelatase, CobN subunit
TIGR02257 (HMM): cobaltochelatase, CobN subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobS subunit11bNOTIGR01651 (HMM): cobaltochelatase, CobT subunit
TIGR01651 (HMM): cobaltochelatase, CobT subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobS subunit11bNOTIGR01651 (HMM): cobaltochelatase, CobT subunit
TIGR01651 (HMM): cobaltochelatase, CobT subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobS subunit11bNOTIGR01651 (HMM): cobaltochelatase, CobT subunit
TIGR01651 (HMM): cobaltochelatase, CobT subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
proposed CobX subunit of cobaltochelatase11bc?NOTIGR02442 (HMM): cobaltochelatase subunit
TIGR02442 (HMM): cobaltochelatase subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
proposed CobX subunit of cobaltochelatase11bc?NOTIGR02442 (HMM): cobaltochelatase subunit
TIGR02442 (HMM): cobaltochelatase subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
proposed CobX subunit of cobaltochelatase11bc?NOTIGR02442 (HMM): cobaltochelatase subunit
TIGR02442 (HMM): cobaltochelatase subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobT subunit11cNOTIGR01650 (HMM): cobaltochelatase, CobS subunit
TIGR01650 (HMM): cobaltochelatase, CobS subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobT subunit11cNOTIGR01650 (HMM): cobaltochelatase, CobS subunit
TIGR01650 (HMM): cobaltochelatase, CobS subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
cobaltochelatase, CobT subunit11cNOTIGR01650 (HMM): cobaltochelatase, CobS subunit
TIGR01650 (HMM): cobaltochelatase, CobS subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
CobW cobaltochelatase-associated protein12NOTIGR02475 (HMM): cobalamin biosynthesis protein CobW
TIGR02475 (HMM): cobalamin biosynthesis protein CobW
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
CobW cobaltochelatase-associated protein12NOTIGR02475 (HMM): cobalamin biosynthesis protein CobW
TIGR02475 (HMM): cobalamin biosynthesis protein CobW
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
CobW cobaltochelatase-associated protein12NOTIGR02475 (HMM): cobalamin biosynthesis protein CobW
TIGR02475 (HMM): cobalamin biosynthesis protein CobW
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
cobalt reductase (NOT BluB)13YES
cobalt reductase (NOT BluB)13YES
cobalt reductase (NOT BluB)13YES
C-20 methylase (CobI)2YESTIGR01467 (HMM): precorrin-2 C(20)-methyltransferase
TIGR01467 (HMM): precorrin-2 C(20)-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-20 methylase (CobI)2YESTIGR01467 (HMM): precorrin-2 C(20)-methyltransferase
TIGR01467 (HMM): precorrin-2 C(20)-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-20 methylase (CobI)2YESTIGR01467 (HMM): precorrin-2 C(20)-methyltransferase
TIGR01467 (HMM): precorrin-2 C(20)-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
precorrin 3B synthase (CobG/CobZ)3YESTIGR02435 (HMM): precorrin-3B synthase
TIGR02485 (HMM): precorrin 3B synthase CobZ
TIGR02435 (HMM): precorrin-3B synthase
TIGR02485 (HMM): precorrin 3B synthase CobZ
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
precorrin 3B synthase (CobG/CobZ)3YESTIGR02435 (HMM): precorrin-3B synthase
TIGR02485 (HMM): precorrin 3B synthase CobZ
TIGR02435 (HMM): precorrin-3B synthase
TIGR02485 (HMM): precorrin 3B synthase CobZ
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
precorrin 3B synthase (CobG/CobZ)3YESTIGR02435 (HMM): precorrin-3B synthase
TIGR02485 (HMM): precorrin 3B synthase CobZ
TIGR02435 (HMM): precorrin-3B synthase
TIGR02485 (HMM): precorrin 3B synthase CobZ
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-17 methylase (CobJ)4YESTIGR01466 (HMM): precorrin-3B C17-methyltransferase
TIGR01466 (HMM): precorrin-3B C17-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-17 methylase (CobJ)4YESTIGR01466 (HMM): precorrin-3B C17-methyltransferase
TIGR01466 (HMM): precorrin-3B C17-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-17 methylase (CobJ)4YESTIGR01466 (HMM): precorrin-3B C17-methyltransferase
TIGR01466 (HMM): precorrin-3B C17-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-11 methylase (CobM)5YESTIGR01465 (HMM): precorrin-4 C11-methyltransferase
TIGR01465 (HMM): precorrin-4 C11-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-11 methylase (CobM)5YESTIGR01465 (HMM): precorrin-4 C11-methyltransferase
TIGR01465 (HMM): precorrin-4 C11-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-11 methylase (CobM)5YESTIGR01465 (HMM): precorrin-4 C11-methyltransferase
TIGR01465 (HMM): precorrin-4 C11-methyltransferase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C1 methylase (CobF)6YESTIGR02434 (HMM): precorrin-6A synthase (deacetylating)
TIGR02434 (HMM): precorrin-6A synthase (deacetylating)
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C1 methylase (CobF)6YESTIGR02434 (HMM): precorrin-6A synthase (deacetylating)
TIGR02434 (HMM): precorrin-6A synthase (deacetylating)
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C1 methylase (CobF)6YESTIGR02434 (HMM): precorrin-6A synthase (deacetylating)
TIGR02434 (HMM): precorrin-6A synthase (deacetylating)
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
precorrin 6 reductase (CobK)7YESTIGR00715 (HMM): precorrin-6x reductase
PF02571 (HMM): precorrin-6x reductase CbiJ/CobK
TIGR00715 (HMM): precorrin-6x reductase
PF02571 (HMM): precorrin-6x reductase CbiJ/CobK
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
precorrin 6 reductase (CobK)7YESTIGR00715 (HMM): precorrin-6x reductase
PF02571 (HMM): precorrin-6x reductase CbiJ/CobK
TIGR00715 (HMM): precorrin-6x reductase
PF02571 (HMM): precorrin-6x reductase CbiJ/CobK
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
precorrin 6 reductase (CobK)7YESTIGR00715 (HMM): precorrin-6x reductase
PF02571 (HMM): precorrin-6x reductase CbiJ/CobK
TIGR00715 (HMM): precorrin-6x reductase
PF02571 (HMM): precorrin-6x reductase CbiJ/CobK
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
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 subunit
TIGR02467 (HMM): precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit
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 subunit
TIGR02467 (HMM): precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit
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 subunit
TIGR02467 (HMM): precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO: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 subunit
TIGR02469 (HMM): precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO: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 subunit
TIGR02469 (HMM): precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO: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 subunit
TIGR02469 (HMM): precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-11, C-12 mutase (CobH)9YESPF02570 (HMM): precorrin-8X methylmutase
PF02570 (HMM): precorrin-8X methylmutase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-11, C-12 mutase (CobH)9YESPF02570 (HMM): precorrin-8X methylmutase
PF02570 (HMM): precorrin-8X methylmutase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process
C-11, C-12 mutase (CobH)9YESPF02570 (HMM): precorrin-8X methylmutase
PF02570 (HMM): precorrin-8X methylmutase
GO:0019250: aerobic cobalamin biosynthetic process
GO:0019250: aerobic cobalamin biosynthetic process

Parent Properties
AccessionName
GenProp0274coenzyme B12 biosynthesis - overview
GenProp0274coenzyme B12 biosynthesis - overview
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)