L-threonine catabolism in Pseudomonas fluorescens GW456-L13

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 (52 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)	PfGW456L13_4606	PfGW456L13_124
braD	L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD)	PfGW456L13_4608	PfGW456L13_123
braE	L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC)	PfGW456L13_4609	PfGW456L13_122
braF	L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA)	PfGW456L13_4610	PfGW456L13_84
braG	L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE)	PfGW456L13_4611	PfGW456L13_120
ltaE	L-threonine aldolase	PfGW456L13_1114	PfGW456L13_2685
adh	acetaldehyde dehydrogenase (not acylating)	PfGW456L13_3517	PfGW456L13_1342
ackA	acetate kinase	PfGW456L13_4820
pta	phosphate acetyltransferase	PfGW456L13_4990
gcvP	glycine cleavage system, P component (glycine decarboxylase)	PfGW456L13_1868	PfGW456L13_904
gcvT	glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)	PfGW456L13_1866	PfGW456L13_902
gcvH	glycine cleavage system, H component (lipoyl protein)	PfGW456L13_903	PfGW456L13_1869
lpd	dihydrolipoyl dehydrogenase	PfGW456L13_3543	PfGW456L13_4267
Alternative steps:
acn	(2R,3S)-2-methylcitrate dehydratase	PfGW456L13_4116	PfGW456L13_3378
acnD	2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)	PfGW456L13_4116	PfGW456L13_4052
acs	acetyl-CoA synthetase, AMP-forming	PfGW456L13_1963	PfGW456L13_1517
ald-dh-CoA	acetaldehyde dehydrogenase, acylating	PfGW456L13_2505
aldA	lactaldehyde dehydrogenase	PfGW456L13_3932	PfGW456L13_2360
D-LDH	D-lactate dehydrogenase	PfGW456L13_5118	PfGW456L13_2028
dddA	3-hydroxypropionate dehydrogenase	PfGW456L13_3561	PfGW456L13_1082
DVU3032	L-lactate dehydrogenase, LutC-like component
DVU3033	L-lactate dehydrogenase, fused LutA/LutB components	PfGW456L13_5116
epi	methylmalonyl-CoA epimerase	PfGW456L13_3114	PfGW456L13_1425
glcD	D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD)
glcE	D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF	D-lactate dehydrogenase, FeS subunit GlcF
gloA	glyoxylase I	PfGW456L13_2929
gloB	hydroxyacylglutathione hydrolase (glyoxalase II)	PfGW456L13_3340	PfGW456L13_1623
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	PfGW456L13_3427	PfGW456L13_2984
iolA	malonate semialdehyde dehydrogenase (CoA-acylating)	PfGW456L13_2	PfGW456L13_5146
kbl	glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)	PfGW456L13_1148
L-LDH	L-lactate dehydrogenase	PfGW456L13_2974
lctB	electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC	electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit	PfGW456L13_2137
lctD	D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO	L-lactate oxidase or 2-monooxygenase
lldE	L-lactate dehydrogenase, LldE subunit	PfGW456L13_5115
lldF	L-lactate dehydrogenase, LldF subunit	PfGW456L13_5116
lldG	L-lactate dehydrogenase, LldG subunit	PfGW456L13_5117
lutA	L-lactate dehydrogenase, LutA subunit	PfGW456L13_5115
lutB	L-lactate dehydrogenase, LutB subunit	PfGW456L13_5116
lutC	L-lactate dehydrogenase, LutC subunit	PfGW456L13_5117
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	PfGW456L13_2284	PfGW456L13_2588
pccA1	propionyl-CoA carboxylase, biotin carboxyl carrier subunit	PfGW456L13_728	PfGW456L13_52
pccA2	propionyl-CoA carboxylase, biotin carboxylase subunit
pccB	propionyl-CoA carboxylase, beta subunit	PfGW456L13_2590	PfGW456L13_2287
pco	propanyl-CoA oxidase	PfGW456L13_554	PfGW456L13_2983
phtA	L-threonine uptake permease PhtA
prpB	2-methylisocitrate lyase	PfGW456L13_4118	PfGW456L13_2633
prpC	2-methylcitrate synthase	PfGW456L13_4117	PfGW456L13_4274
prpD	2-methylcitrate dehydratase	PfGW456L13_4114
prpF	methylaconitate isomerase	PfGW456L13_4115
RR42_RS28305	L-threonine:H+ symporter	PfGW456L13_4790	PfGW456L13_318
serP1	L-threonine uptake transporter SerP1	PfGW456L13_4291	PfGW456L13_4400
snatA	L-threonine transporter snatA	PfGW456L13_60
sstT	L-threonine:Na+ symporter SstT	PfGW456L13_2541
tdcB	L-threonine dehydratase	PfGW456L13_949	PfGW456L13_3031
tdcC	L-threonine:H+ symporter TdcC	PfGW456L13_3379
tdcE	2-ketobutyrate formate-lyase
tdh	L-threonine 3-dehydrogenase	PfGW456L13_3512	PfGW456L13_1214
tynA	aminoacetone oxidase	PfGW456L13_2439
yvgN	methylglyoxal reductase (NADPH-dependent)	PfGW456L13_2401	PfGW456L13_1417

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.