L-threonine catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd

Also see fitness data for the top candidates

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 (53 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
braC	L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)	Pf1N1B4_3218	Pf1N1B4_1382
braD	L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD)	Pf1N1B4_3217	Pf1N1B4_1381
braE	L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC)	Pf1N1B4_3216	Pf1N1B4_1380
braF	L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA)	Pf1N1B4_3215	Pf1N1B4_1346
braG	L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE)	Pf1N1B4_3214	Pf1N1B4_1378
ltaE	L-threonine aldolase	Pf1N1B4_2451	Pf1N1B4_2778
adh	acetaldehyde dehydrogenase (not acylating)	Pf1N1B4_4502	Pf1N1B4_2673
ackA	acetate kinase	Pf1N1B4_879
pta	phosphate acetyltransferase	Pf1N1B4_1055
gcvP	glycine cleavage system, P component (glycine decarboxylase)	Pf1N1B4_621	Pf1N1B4_2236
gcvT	glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)	Pf1N1B4_623	Pf1N1B4_2234
gcvH	glycine cleavage system, H component (lipoyl protein)	Pf1N1B4_2235	Pf1N1B4_620
lpd	dihydrolipoyl dehydrogenase	Pf1N1B4_4477	Pf1N1B4_3683
Alternative steps:
acn	(2R,3S)-2-methylcitrate dehydratase	Pf1N1B4_3821	Pf1N1B4_4564
acnD	2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)	Pf1N1B4_3821	Pf1N1B4_3888
acs	acetyl-CoA synthetase, AMP-forming	Pf1N1B4_3430	Pf1N1B4_2849
ald-dh-CoA	acetaldehyde dehydrogenase, acylating
aldA	lactaldehyde dehydrogenase	Pf1N1B4_5695	Pf1N1B4_171
D-LDH	D-lactate dehydrogenase	Pf1N1B4_1190	Pf1N1B4_3500
dddA	3-hydroxypropionate dehydrogenase	Pf1N1B4_4450	Pf1N1B4_2416
DVU3032	L-lactate dehydrogenase, LutC-like component
DVU3033	L-lactate dehydrogenase, fused LutA/LutB components	Pf1N1B4_1188
epi	methylmalonyl-CoA epimerase
glcD	D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD)	Pf1N1B4_5862	Pf1N1B4_2274
glcE	D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)	Pf1N1B4_5863
glcF	D-lactate dehydrogenase, FeS subunit GlcF	Pf1N1B4_5864
gloA	glyoxylase I	Pf1N1B4_5009
gloB	hydroxyacylglutathione hydrolase (glyoxalase II)	Pf1N1B4_4596	Pf1N1B4_2963
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	Pf1N1B4_4788	Pf1N1B4_5593
iolA	malonate semialdehyde dehydrogenase (CoA-acylating)	Pf1N1B4_4277	Pf1N1B4_1238
kbl	glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)	Pf1N1B4_2488
L-LDH	L-lactate dehydrogenase	Pf1N1B4_4705	Pf1N1B4_5979
lctB	electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC	electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit	Pf1N1B4_391	Pf1N1B4_5613
lctD	D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component	Pf1N1B4_5862	Pf1N1B4_2274
lctO	L-lactate oxidase or 2-monooxygenase
lldE	L-lactate dehydrogenase, LldE subunit	Pf1N1B4_1187
lldF	L-lactate dehydrogenase, LldF subunit	Pf1N1B4_1188
lldG	L-lactate dehydrogenase, LldG subunit	Pf1N1B4_1189
lutA	L-lactate dehydrogenase, LutA subunit	Pf1N1B4_1187
lutB	L-lactate dehydrogenase, LutB subunit	Pf1N1B4_1188
lutC	L-lactate dehydrogenase, LutC subunit	Pf1N1B4_1189
mcm-large	methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small	methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA	methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA	propionyl-CoA carboxylase, alpha subunit	Pf1N1B4_225	Pf1N1B4_3984
pccA1	propionyl-CoA carboxylase, biotin carboxyl carrier subunit	Pf1N1B4_2010	Pf1N1B4_1309
pccA2	propionyl-CoA carboxylase, biotin carboxylase subunit
pccB	propionyl-CoA carboxylase, beta subunit	Pf1N1B4_3986	Pf1N1B4_222
pco	propanyl-CoA oxidase	Pf1N1B4_1816
phtA	L-threonine uptake permease PhtA
prpB	2-methylisocitrate lyase	Pf1N1B4_3819	Pf1N1B4_4042
prpC	2-methylcitrate synthase	Pf1N1B4_3820	Pf1N1B4_3676
prpD	2-methylcitrate dehydratase	Pf1N1B4_3823
prpF	methylaconitate isomerase	Pf1N1B4_3822	Pf1N1B4_4463
RR42_RS28305	L-threonine:H+ symporter	Pf1N1B4_801	Pf1N1B4_1580
serP1	L-threonine uptake transporter SerP1	Pf1N1B4_4976	Pf1N1B4_1580
snatA	L-threonine transporter snatA	Pf1N1B4_1320
sstT	L-threonine:Na+ symporter SstT	Pf1N1B4_3934
tdcB	L-threonine dehydratase	Pf1N1B4_2280	Pf1N1B4_4257
tdcC	L-threonine:H+ symporter TdcC	Pf1N1B4_4562	Pf1N1B4_1014
tdcE	2-ketobutyrate formate-lyase
tdh	L-threonine 3-dehydrogenase	Pf1N1B4_3270	Pf1N1B4_4506
tynA	aminoacetone oxidase
yvgN	methylglyoxal reductase (NADPH-dependent)	Pf1N1B4_128	Pf1N1B4_85

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 17 2021. The underlying query database was built on Sep 17 2021.