L-valine catabolism in Chlorobium phaeobacteroides BS1

Best path

Bap2, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small

Rules

Overview: Valine degradation in GapMind is based on MetaCyc pathway L-valine degradation I (link). The other pathways do not produce any fixed carbon and are not included.

• all: valine-transport, BKD, acdH, ech, bch, mmsB, mmsA and propionyl-CoA-degradation
  • Comment: An aminotransferase (not represented) forms 3-methyl-2-oxobutanoate, the decarboxylating alpha-ketoacid dehydrogenase (BKD) forms isobutanoyl-CoA, dehydrogenase acdH forms methylacrylyl-CoA (2-methylprop-2-enoyl-CoA), the hydratase ech forms (S)-3-hydroxy-isobutaonoyl-CoA, a hydrolase forms (S)-3-hydroxy-isobutanoate, a dehydrogenase forms (S)-methylmalonate semialdehyde (2-methyl-3-oxopropanoate), and a decarboxylating dehydrogenase forms propionyl-CoA.
• BKD:
  • bkdA, bkdB, bkdC and lpd
  • or vorA, vorB and vorC
  • or ofoA and ofoB
  • or ofo
  • Comment: These decarboxylating dehydrogenases act on 4-methyl-2-oxopentanoate, 3-methyl-2-oxobutanoate (2-oxoisovalerate) and (S)-3-methyl-2-oxopentanoate and are known as the branched-chain alpha-ketoacid dehydrogenases. They can pass electrons to NAD (EC 1.2.1.25) or to ferredoxin (EC 1.2.7.7). The NAD-dependent enzyme is the sum of three activities: EC 1.2.4.4 (the 4-methyl-2-oxopentanoate dehydrogenase, with transfer to the lipopoyllysine residue of 2.3.1.168) which is itself heteromeric, with alpha and beta subunits; EC 2.3.1.168 (dihydrolipoyllysine-residue (3-methylbutanoyl)transferase); and EC 1.8.1.4 (dihydrolipoyl dehydrogenase, transferring electrons to NAD). The well-characterized ferredoxin-dependent enzymes have 3 subunits (vorABC) or 2 subunits (ofoAB). Genetic data identified a fused ferredoxin-dependent enzyme with just 1 subunit (ofo).
• propionyl-CoA-degradation:
  • prpC, prpD, acn and prpB
  • or prpC, acnD, prpF, acn and prpB
  • or propionyl-CoA-carboxylase, epi and methylmalonyl-CoA-mutase
  • or pco, hpcD, dddA and iolA
  • Comment: In 2-methylcitrate cycle I, propionyl-CoA is combined with oxalacetate (by prpC) to give methylcitrate, dehydrated to cis-2-methylaconitate by prpD, hydrated to (2R,3S)-2-methylisocitrate, and a lyase produces pyruvate and succinate. (We consider succinate as a central intermediate, as most organisms can activate it to succinyl-CoA or can oxidize it to fumarate and convert that to oxaloacetate.) In 2-methylcitrate cycle II, a different dehydratase (acnD) and an isomerase (prpF) replace the dehydratase prpD; acnD dehydrates (2S,3S)-2-methylcitrate to 2-methyl-trans-aconitate, and prpF isomerizes it to cis-2-methylaconitate. In propanoyl CoA degradation I, propionyl-CoA carboxylase forms (S)-methylmalonyl-CoA, methylmalonyl-CoA epimerase forms (R)-methylmalonyl-CoA, and methylmalonyl-CoA mutase forms succinyl-CoA, which is a central metabolite. (Note that methylmalonyl-CoA mutase requires adenosylcobamide, a form of vitamin B12, for activity.) In propanoyl-CoA degradation II: propionyl-CoA is oxidized to acrylyl-CoA by pco, hydrated to 3-hydroxypropionyl-CoA, hydrolzed to 3-hydroxypropionate, oxidized to 3-oxopropionate (malonate semialdehyde), and oxidized to acetyl-CoA and CO2.
• methylmalonyl-CoA-mutase:
  • mcmA
  • or mcm-large and mcm-small
  • Comment: methylmalonyl-CoA mutase has a catalytic domain and a B12-binding domain. These are usually found in the same protein, which we call mcmA. In Metallosphaera and Pyrococcus, the B12-binding domain is a separate subunit. In Propionibacterium and Methylorubrum, there is an additional subunit with a catalytic domain only; this may have a protective role (PMID:14734568) and is not described here. There's also a mcm-interacting GTPase (known as MeaB or YgfD) that loads B12 onto mcm and protects it from inactivation (see PMC4631608); this is not described here. Some fused mcm proteins include a MeaB domain as well (i.e., Q8F222, Q8Y2U5).
• propionyl-CoA-carboxylase:
  • pccA and pccB
  • or pccA1, pccA2 and pccB
  • Comment: propionyl-CoA carboxylase is a heteromer, usually with alpha and beta subunits pccAB. Haloferax mediterranei has a third subunit as well (pccX), which is not described here. Acidianus brierleyi has a diverged pccA split into two pieces.
• valine-transport:
  • livF, livG, livJ, livH and livM
  • or natA, natB, natC, natD and natE
  • or Bap2
  • or brnQ
  • or phtJ
  • or bcaP
  • Comment: Transporters were identified using query: transporter:valine:L-valine:val

47 steps (26 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
Bap2	L-valine permease Bap2
ofo	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH	isobutyryl-CoA dehydrogenase
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	Cphamn1_2077	Cphamn1_2111
bch	3-hydroxyisobutyryl-CoA hydrolase	Cphamn1_2111
mmsB	3-hydroxyisobutyrate dehydrogenase	Cphamn1_2105
mmsA	methylmalonate-semialdehyde dehydrogenase	Cphamn1_2056
pccA	propionyl-CoA carboxylase, alpha subunit	Cphamn1_0321
pccB	propionyl-CoA carboxylase, beta subunit
epi	methylmalonyl-CoA epimerase	Cphamn1_1175
mcm-large	methylmalonyl-CoA mutase, large (catalytic) subunit	Cphamn1_1173
mcm-small	methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit	Cphamn1_1173	Cphamn1_2093
Alternative steps:
acn	(2R,3S)-2-methylcitrate dehydratase	Cphamn1_1817	Cphamn1_2466
acnD	2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)	Cphamn1_2466
bcaP	L-valine uptake transporter BcaP/CitA
bkdA	branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB	branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC	branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ	L-valine:cation symporter BrnQ/BraZ/BraB
dddA	3-hydroxypropionate dehydrogenase
hpcD	3-hydroxypropionyl-CoA dehydratase	Cphamn1_2111	Cphamn1_2077
iolA	malonate semialdehyde dehydrogenase (CoA-acylating)
livF	L-valine ABC transporter, ATPase component 1 (LivF/BraG)	Cphamn1_0700	Cphamn1_2170
livG	L-valine ABC transporter, ATPase component 2 (LivG/BraF)	Cphamn1_2170	Cphamn1_0699
livH	L-valine ABC transporter, permease component 1 (LivH/BraD)
livJ	L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM	L-valine ABC transporter, permease component 2 (LivM/BraE)	Cphamn1_0698
lpd	branched-chain alpha-ketoacid dehydrogenase, E3 component	Cphamn1_1045	Cphamn1_1481
mcmA	methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components	Cphamn1_1173
natA	L-valine ABC transporter, ATPase component 1 (NatA)	Cphamn1_0699	Cphamn1_2170
natB	L-valine ABC transporter, substrate-binding component NatB
natC	L-valine ABC transporter, permease component 1 (NatC)
natD	L-valine ABC transporter, permease component 2 (NatD)
natE	L-valine ABC transporter, ATPase component 2 (NatE)	Cphamn1_2170	Cphamn1_0700
ofoA	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA	Cphamn1_1033
ofoB	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB	Cphamn1_1034	Cphamn1_0326
pccA1	propionyl-CoA carboxylase, biotin carboxyl carrier subunit	Cphamn1_0321
pccA2	propionyl-CoA carboxylase, biotin carboxylase subunit	Cphamn1_1200
pco	propanyl-CoA oxidase	Cphamn1_0670
phtJ	L-valine uptake permease PhtJ
prpB	2-methylisocitrate lyase
prpC	2-methylcitrate synthase	Cphamn1_2068
prpD	2-methylcitrate dehydratase
prpF	methylaconitate isomerase
vorA	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA	Cphamn1_0326
vorB	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB	Cphamn1_1033
vorC	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.