L-isoleucine catabolism in Desulfitobacterium hafniense DCB-2

Best path

brnQ, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small

Rules

Overview: Isoleucine degradation in GapMind is based on MetaCyc pathway L-isoleucine degradation I (link). The other pathways are fermentative and do not lead to carbon incorporation (link, link).

• all: isoleucine-transport, BKD, acdH, ech, ivdG, fadA and propionyl-CoA-degradation
  • Comment: A transaminase (which is not represented) converts isoleucine to (3S)-3-methyl-2-oxopentanoate, the decarboxylating dehydrogenase BKD forms (2S)-2-methylbutanoyl-CoA, dehydrogenase acdH forms (E)-2-methylcrotonyl-CoA, hydratase ech forms (2S,3S)-3-hydroxy-2-methylbutanoyl-CoA, dehydrogenase ivdG forms 2-methylacetoacetyl-CoA, and a thiolase forms propanioyl-CoA and acetyl-CoA. (The initial transaminase is not represented because amino-acid aminotransferases are often non-specific.)
• 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.
• isoleucine-transport:
  • livF, livG, livJ, livH and livM
  • or natA, natB, natC, natD and natE
  • or Bap2
  • or brnQ
  • or bcaP
  • Comment: Transporters were identified using query: transporter:isoleucine:L-isoleucine:ile and non-specific large neutral amino acid tranpsorters from mammals were ignored.

45 steps (22 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
brnQ	L-isoleucine:cation symporter BrnQ/BraZ/BraB	DHAF_RS11265
ofo	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH	(2S)-2-methylbutanoyl-CoA dehydrogenase	DHAF_RS14315	DHAF_RS14305
ech	2-methyl-3-hydroxybutyryl-CoA hydro-lyase	DHAF_RS14270	DHAF_RS18210
ivdG	3-hydroxy-2-methylbutyryl-CoA dehydrogenase	DHAF_RS19070	DHAF_RS03090
fadA	2-methylacetoacetyl-CoA thiolase	DHAF_RS03095	DHAF_RS14275
pccA	propionyl-CoA carboxylase, alpha subunit	DHAF_RS17500
pccB	propionyl-CoA carboxylase, beta subunit
epi	methylmalonyl-CoA epimerase
mcm-large	methylmalonyl-CoA mutase, large (catalytic) subunit	DHAF_RS13500
mcm-small	methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit	DHAF_RS13505	DHAF_RS14625
Alternative steps:
acn	(2R,3S)-2-methylcitrate dehydratase
acnD	2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2	L-isoleucine permease Bap2	DHAF_RS12190	DHAF_RS06640
bcaP	L-isoleucine 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
dddA	3-hydroxypropionate dehydrogenase
hpcD	3-hydroxypropionyl-CoA dehydratase	DHAF_RS14270	DHAF_RS18210
iolA	malonate semialdehyde dehydrogenase (CoA-acylating)	DHAF_RS13220
livF	L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG)	DHAF_RS24525	DHAF_RS05220
livG	L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF)	DHAF_RS24530	DHAF_RS11205
livH	L-isoleucine ABC transporter, permease component 1 (LivH/BraD)	DHAF_RS24540
livJ	L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM	L-isoleucine ABC transporter, permease component 2 (LivM/BraE)	DHAF_RS24535
lpd	branched-chain alpha-ketoacid dehydrogenase, E3 component	DHAF_RS20325
mcmA	methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components	DHAF_RS13500
natA	L-isoleucine ABC transporter, ATPase component 1 (NatA)	DHAF_RS24530	DHAF_RS24525
natB	L-isoleucine ABC transporter, substrate-binding component NatB
natC	L-isoleucine ABC transporter, permease component 1 (NatC)
natD	L-isoleucine ABC transporter, permease component 2 (NatD)
natE	L-isoleucine ABC transporter, ATPase component 2 (NatE)	DHAF_RS24525	DHAF_RS19415
ofoA	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
pccA1	propionyl-CoA carboxylase, biotin carboxyl carrier subunit	DHAF_RS17500
pccA2	propionyl-CoA carboxylase, biotin carboxylase subunit
pco	propanyl-CoA oxidase	DHAF_RS19060	DHAF_RS14305
prpB	2-methylisocitrate lyase
prpC	2-methylcitrate synthase	DHAF_RS04540
prpD	2-methylcitrate dehydratase
prpF	methylaconitate isomerase
vorA	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.