L-threonine catabolism in Dyella jiangningensis SBZ3-12

Best path

serP1, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd

Rules

Overview: L-threonine degradation in GapMind is based on MetaCyc pathway I via 2-ketobutyrate formate-lyase (link), pathway II via glycine (link), pathway III via methylglyoxal (link), and pathway IV via threonine aldolase (link). Pathway V is not thought to occur in prokaryotes and is not included.

• all:
  • threonine-transport, tdcB, tdcE and propionyl-CoA-degradation
  • or threonine-transport, tdh, kbl and glycine-degradation
  • or threonine-transport, tdh, tynA and methylglyoxal-degradation
  • or threonine-transport, ltaE, acetaldehyde-degradation and glycine-degradation
  • Comment: In L-threonine degradation I, threonine dehydratase (tdcB) forms 2-iminbutanoate, which is deaminated to 2-oxobutanoate (either by the same enzyme or by ridA); then formate-lyase (tdcE) converts this to propanoyl-CoA. (MetaCyc also includes conversion to propanoate, which forms ATP, but this does not allow for growth unless the formate can be utilized.) In L-threonine degradation II, a dehydrogenase (tdh) forms L-2-amino-3-oxobutanoate, and a C-acetyltransferase (kbl) cleaves this to acetyl-CoA and glycine. In L-threonine degradation III, tdh forms L-2-amino-3-oxobutanoate, and oxidase tynA forms methylglyoxal. In L-threonine degradation IV, aldolase ltaE cleaves threonine to acetaldehyde and glycine.
• L-lactate-degradation:
  • L-LDH
  • or lldE, lldF and lldG
  • or lutA, lutB and lutC
  • or DVU3033 and DVU3032
  • or lctO and acs
  • or lctO, ackA and pta
  • Comment: Various L-lactate dehydrogenases are known, with different numbers of subunits; these all form pyruvate. Or, after L-lactate oxidase (lctO) forms acetate, the acetate is activated to acetyl-CoA.
• methylglyoxal-degradation:
  • gloA, gloB and D-lactate-dehydrogenase
  • or yvgN, aldA and L-lactate-degradation
  • Comment: In methylglyoxal degradation I (link), gloA condenses methylglyoxal with glutathione to (R)-S-lactoylglutathione, gloB cleaves it to D-lactate (also known as (R)-lactate) and glutathione, and the lactate is oxidized to pyruvate. In methylglyoxal degradation IV (link), yvgN reduces methylglyoxal to (S)-lactaldehyde, aldA oxidizes it to (S)-lactate (also known as L-lactate).
• D-lactate-dehydrogenase:
  • D-LDH
  • or lctB, lctC and lctD
  • or glcD, glcE and glcF
  • Comment: Acetobacterium woodii uses an electron-bifurcating dehydrogenase (lctBCD) for growth on lactate. The Km for D-lactate is far below that for L-lactate (Km of 3.6 mM vs. 112 mM; PMID:24762045), so we consider it to be a D-lactate dehydrogenase. GlcDEF from E. coli (EC 1.1.99.14) is usually described as glycolate dehydrogenase or glycolate oxidase, but it has similar activity on D-lactate (PMID:4557653), and homologs from various Proteobacteria are important for D-lactate utilization. The physiological electron acceptor is not known, so terming GlcDEF an oxidase is questionable.
• glycine-degradation:
  • glycine-reductase and ackA
  • or glycine-reductase and pta
  • or gcvP, gcvT, gcvH and lpd
  • Comment: Glycine can be reduced to acetyl phosphate by glycine reductase (EC 1.21.4.2), and then converted to acetate (by ackA in reverse) or acetyl-CoA (by pta) Or glycine can cleaved to ammonia, CO2, and 5,10-methylene-tetrahydrofolate by the glycine cleavage system, gcvPTH/lpd.
• glycine-reductase: grdA, grdE, grdB, grdD and grdC
• acetaldehyde-degradation:
  • ald-dh-CoA
  • or adh and acs
  • or adh, ackA and pta
  • Comment: Acetaldehyde can be oxidized to acetyl-CoA, or oxidized to acetate and activated to acetyl-CoA by either acetyl-CoA synthetase (acs) or by acetate kinase (ackA) and phosphate acetyltransferase (pta).
• 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.
• threonine-transport:
  • braC, braD, braE, braF and braG
  • or tdcC
  • or sstT
  • or serP1
  • or phtA
  • or snatA
  • or RR42_RS28305
  • Comment: Transporters were identified using query: transporter:threonine:L-threonine:thr

70 steps (45 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
serP1	L-threonine uptake transporter SerP1	BLQ78_RS03050	BLQ78_RS08805
ltaE	L-threonine aldolase	BLQ78_RS11395	BLQ78_RS10000
adh	acetaldehyde dehydrogenase (not acylating)	BLQ78_RS18120	BLQ78_RS22185
acs	acetyl-CoA synthetase, AMP-forming	BLQ78_RS13905	BLQ78_RS05135
gcvP	glycine cleavage system, P component (glycine decarboxylase)	BLQ78_RS05340
gcvT	glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)	BLQ78_RS11630
gcvH	glycine cleavage system, H component (lipoyl protein)	BLQ78_RS11625
lpd	dihydrolipoyl dehydrogenase	BLQ78_RS00055	BLQ78_RS17715
Alternative steps:
ackA	acetate kinase	BLQ78_RS18285	BLQ78_RS21345
acn	(2R,3S)-2-methylcitrate dehydratase	BLQ78_RS05190	BLQ78_RS03795
acnD	2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)	BLQ78_RS05190	BLQ78_RS03800
ald-dh-CoA	acetaldehyde dehydrogenase, acylating
aldA	lactaldehyde dehydrogenase	BLQ78_RS04710	BLQ78_RS07900
braC	L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
braD	L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD)
braE	L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC)
braF	L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA)	BLQ78_RS16735	BLQ78_RS10300
braG	L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE)	BLQ78_RS16735	BLQ78_RS12880
D-LDH	D-lactate dehydrogenase	BLQ78_RS09140	BLQ78_RS01155
dddA	3-hydroxypropionate dehydrogenase	BLQ78_RS04725	BLQ78_RS11605
DVU3032	L-lactate dehydrogenase, LutC-like component
DVU3033	L-lactate dehydrogenase, fused LutA/LutB components
epi	methylmalonyl-CoA epimerase
glcD	D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD)	BLQ78_RS01155	BLQ78_RS09140
glcE	D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)	BLQ78_RS01155
glcF	D-lactate dehydrogenase, FeS subunit GlcF	BLQ78_RS02180
gloA	glyoxylase I	BLQ78_RS08820	BLQ78_RS10970
gloB	hydroxyacylglutathione hydrolase (glyoxalase II)	BLQ78_RS07605	BLQ78_RS22270
grdA	glycine reductase component A1
grdB	glycine reductase component B, gamma subunit
grdC	glycine reductase component C, beta subunit
grdD	glycine reductase component C, alpha subunit
grdE	glycine reductase component B, precursor to alpha/beta subunits
hpcD	3-hydroxypropionyl-CoA dehydratase	BLQ78_RS19345	BLQ78_RS15090
iolA	malonate semialdehyde dehydrogenase (CoA-acylating)	BLQ78_RS22185	BLQ78_RS04710
kbl	glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)	BLQ78_RS05215	BLQ78_RS11160
L-LDH	L-lactate dehydrogenase	BLQ78_RS02575
lctB	electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC	electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit	BLQ78_RS11700
lctD	D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component	BLQ78_RS01155	BLQ78_RS09140
lctO	L-lactate oxidase or 2-monooxygenase	BLQ78_RS02575
lldE	L-lactate dehydrogenase, LldE subunit
lldF	L-lactate dehydrogenase, LldF subunit
lldG	L-lactate dehydrogenase, LldG subunit
lutA	L-lactate dehydrogenase, LutA subunit
lutB	L-lactate dehydrogenase, LutB subunit
lutC	L-lactate dehydrogenase, LutC subunit
mcm-large	methylmalonyl-CoA mutase, large (catalytic) subunit	BLQ78_RS14840
mcm-small	methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit	BLQ78_RS14840	BLQ78_RS04615
mcmA	methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components	BLQ78_RS14840
pccA	propionyl-CoA carboxylase, alpha subunit	BLQ78_RS15105	BLQ78_RS10715
pccA1	propionyl-CoA carboxylase, biotin carboxyl carrier subunit	BLQ78_RS10715	BLQ78_RS15105
pccA2	propionyl-CoA carboxylase, biotin carboxylase subunit
pccB	propionyl-CoA carboxylase, beta subunit	BLQ78_RS14980
pco	propanyl-CoA oxidase	BLQ78_RS04735	BLQ78_RS04630
phtA	L-threonine uptake permease PhtA
prpB	2-methylisocitrate lyase	BLQ78_RS15710	BLQ78_RS05140
prpC	2-methylcitrate synthase	BLQ78_RS05145	BLQ78_RS01960
prpD	2-methylcitrate dehydratase	BLQ78_RS05195
prpF	methylaconitate isomerase	BLQ78_RS05185
pta	phosphate acetyltransferase	BLQ78_RS00180
RR42_RS28305	L-threonine:H+ symporter	BLQ78_RS08805	BLQ78_RS03050
snatA	L-threonine transporter snatA	BLQ78_RS09320
sstT	L-threonine:Na+ symporter SstT
tdcB	L-threonine dehydratase	BLQ78_RS11230	BLQ78_RS11120
tdcC	L-threonine:H+ symporter TdcC
tdcE	2-ketobutyrate formate-lyase
tdh	L-threonine 3-dehydrogenase	BLQ78_RS05225	BLQ78_RS21280
tynA	aminoacetone oxidase
yvgN	methylglyoxal reductase (NADPH-dependent)	BLQ78_RS12950

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.