4-hydroxybenzoate catabolism in Sulfuritalea hydrogenivorans DSM 22779

Best path

pcaK, hcl, hcrA, hcrB, hcrC, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB

Rules

Overview: 4-hydroxybenzoate catabolism in GapMind is based on aerobic oxidation to 3,4-hydroxybenzoate (protocatechuate), followed by meta, ortho, or para cleavage; or reduction to benzoyl-CoA (part of a MetaCyc pathway for phenol degradation, link)

• all:
  • 4-hydroxybenzoate-transport, pobA and protocatechuate-degradation
  • or 4-hydroxybenzoate-transport, hcl, hcrA, hcrB, hcrC and benzoyl-CoA-degradation
  • Comment: An aerobic route for degradation of 4-hydroxybenzoate involves 4-hydroxybenzoate 3-monooxygenase pobA, which forms protocatechuate (3,4-dihydroxybenzoate). Alternatively, 4-hydroxybenzoate can be activated to 4-hydroxybenzoyl-CoA by hcl and reduced to benzoyl-CoA by hcrABC (link).
• protocatechuate-degradation:
  • ligA, ligB, ligC, ligI, ligU, ligJ and ligK
  • or pcaH, pcaG, pcaB, pcaC, pcaD and 3-oxoadipate-degradation
  • or praA and 2-hydroxymuconate-6-semialdehyde-degradation
  • Comment: In the meta-cleavage pathway (link), the 4,5-dioxygenase ligAB splits protocatechuate to 4-carboxy-2-hydroxymuconate-6-semialdehyde. (In solution, this is in the hemiacetal form.) The semialdehyde is oxidized to 2-pyrone-4,6-dicarboxylate, hydrolyzed to (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate, tautomerized to (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate, hydrated to 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate (4-oxalocitramalate), and split by an aldolase to pyruvate and oxaloacetate. In the ortho-cleavage pathway (link), the 3,4-oxygenase pcaHG cleaves the ring to 3-carboxy-cis,cis-muconate, a cycloisomerase forms 4-carboxymuconolactone (2-carboxy-2,5-dihydro-5-oxofuran-2-yl)-acetate), a decarboxylase forms 3-oxoadipate enol lactone ((4,5-dihydro-5-oxofuran-2-yl)-acetate), and a hydrolase forms 3-oxoadipate. In the para-cleavage pathway (link), the 2,3-dioxygenase praA forms (2Z,4Z)-2-hydroxy-5-carboxymuconate-6-semialdehyde, which spontaneously decarboxylates to (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate, also known as 2-hydroxymuconate 6-semialdehyde.
• 2-hydroxymuconate-6-semialdehyde-degradation:
  • praB, praC, praD and 2-hydroxypenta-2,4-dienoate-degradation
  • or xylF and 2-hydroxypenta-2,4-dienoate-degradation
  • Comment: Dehydrogenase praB forms 2-hydroxymuconate, tautomerase praC forms (3E)-2-oxohex-3-enedioate (2-oxalocrotonate), and decarboxylase praD yields 2-hydroxypenta-2,4-dienoate (HPD). (This series of steps is part of protocatechuate para-cleavage, link, or catechol degradation II, link.) Or, hydrolase xylF forms HPD and formate. (This is part of a MetaCyc pathway for catechol degradation, link.)
• benzoyl-CoA-degradation:
  • benzoyl-CoA-reductase, dch, had, oah, pimB and glutaryl-CoA-degradation
  • or benzoyl-CoA-reductase, Ch1CoA, badK, badH, badI, pimD, pimC, pimF and glutaryl-CoA-degradation
  • or boxA, boxB, boxC, boxD, paaF, paaH and paaJ2
  • Comment: Benzoyl-CoA can be degraded anaerobically (link) by reduction to cyclohex-1,5-diene-1-carbonyl-CoA, followed by hydratase (dch) to 6-hydroxycyclohex-1-ene-1-carbonyl-CoA, a dehydrogenase to 6-oxocyclohex-1-ene-1-carbonyl-CoA, a hydrolase to 2-hydroxy-6-oxocycloheane-1-carbonyl-CoA, a ring-opening hydrolase to 3-hydroxypimeloyl-CoA [the last two steps are both catalyzed by oah], a dehydrogenase to 3-oxopimeloyl-CoA [not linked to sequence and omitted], and an acetyltransferase to glutaryl-CoA and acetyl-CoA. Alternatively, after reduction to cyclohex-1,5-diene-1-carbonyl-CoA, Ch1CoA can further reduce it to cyclohex-1-ene-1-carboxyl-CoA (link), followed by hydration to 2-hydroxy-cyclohexane-1-carbonyl-CoA, oxidation to 2-ketocyclohexane-1-carbonyl-CoA, cleavage by a ring-opening hydrolase to pimeloyl-CoA, oxidation to 2,3-didehydropimeloyl-CoA, hydration to 3-hydroxypimeloyl-C, oxidation to 3-oxopimeloyl-CoA and cleavage by a thiolase to glutaryl-CoA and acetyl-CoA. Benzoyl-CoA degradation can be degraded aerobically (link) by an epoxidase (boxAB) that forms 2,3-epoxy-2-3-dihydrobenzoyl-CoA; a dihydrolase forms cis-3,4-dihydroadipyl-CoA semialdehyde and formate; a dehydrogenase forms cis-3,4-dehydroadipyl-CoA; and an unknown isomerase forms trans-2,3-dehydroadipyl-CoA. This is converted to succinyl-CoA as in the anaerobic pathway (paaF, paaH, and paaJ2).
• glutaryl-CoA-degradation: gcdH, ech, fadB and atoB
  • Comment: In MetaCyc pathway glutaryl-CoA degradation (link), glutaryl-CoA is oxidized to (E)-glutaconyl-CoA and oxidatively decarboxylated to crotonyl-CoA (both by the same enzyme), hydrated to 3-hydroxybutanoyl-CoA, oxidized to acetoacetyl-CoA, and cleaved to two acetyl-CoA.
• benzoyl-CoA-reductase:
  • bcrA, bcrB, bcrC and bcrD
  • or bamB, bamC, bamD, bamE, bamF, bamG, bamH and bamI
  • Comment: Benzoyl-CoA reduction is energetically unfavorable. There are two classes of reductases: class I enzymes (bcrABCD) use ATP to drive the reaction, while class II enzymes (bamBCDEFGHI) are thought to us an electron bifurcation. SYN_02587 (Q2LQN9) from Syntrophus aciditrophicus, which can oxidize cyclohex-1,5-diene-1-carbonyl-CoA to benzoyl-CoA, is not included because it seems to lack a mechanism to drive benzoyl-CoA reduction.
• 2-hydroxypenta-2,4-dienoate-degradation: mhpD, mhpE and acetaldehyde-degradation
  • Comment: (2Z)-2-hydroxypenta-2,4-dienoate (HPD) is a common intermediate in the aerobic degradation of many aromatic compounds. In MetaCyc pathway 2-hydroxypenta-2,4-dienoate degradation (link), HPD is hydrated to (S)-4-hydroxy-2-oxopentanoate and an aldolase cleaves it to pyruvate and acetaldehyde.
• 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).
• 3-oxoadipate-degradation: 3-oxodipate-CoA-transferase and pcaF
  • Comment: MetaCyc pathway 3-oxoadipate degradation (link) involves activation by CoA (using succinyl-CoA) and a thiolase (succinyltransferase) reaction that splits it to acetyl-CoA and succinyl-CoA.
• 3-oxodipate-CoA-transferase:
  • pcaI and pcaJ
  • or catI and catJ
  • Comment: Two different types of 3-oxoadipate CoA-transferases (EC 2.8.3.6) are known. They are both heteromeric with each subunit containing a CoA-transferase domain
• 4-hydroxybenzoate-transport:
  • pcaK
  • or fcbT1, fcbT2 and fcbT3
  • Comment: Transporters were identified using: query: transporter:4-hydroxybenzoate:p-hydroxybenzoate:4-hydroxybenzoic acid:p-hydroxybenzoic acid

72 steps (46 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
pcaK	4-hydroxybenzoate transporter pcaK
hcl	4-hydroxybenzoyl-CoA ligase	SUTH_RS08240	SUTH_RS06995
hcrA	4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB	4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC	4-hydroxybenzoyl-CoA reductase, gamma subunit
bcrA	ATP-dependent benzoyl-CoA reductase, alpha subunit	SUTH_RS08185	SUTH_RS08180
bcrB	ATP-dependent benzoyl-CoA reductase, beta subunit	SUTH_RS08175
bcrC	ATP-dependent benzoyl-CoA reductase, gamma subunit	SUTH_RS08170
bcrD	ATP-dependent benzoyl-CoA reductase, delta subunit	SUTH_RS08180	SUTH_RS08185
dch	cyclohexa-1,5-diene-1-carboxyl-CoA hydratase	SUTH_RS08215	SUTH_RS08545
had	6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase	SUTH_RS08220
oah	6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase	SUTH_RS08225
pimB	3-oxopimeloyl-CoA:CoA acetyltransferase	SUTH_RS05630	SUTH_RS07380
gcdH	glutaryl-CoA dehydrogenase	SUTH_RS08235	SUTH_RS02660
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	SUTH_RS15075	SUTH_RS08215
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	SUTH_RS07375	SUTH_RS03100
atoB	acetyl-CoA C-acetyltransferase	SUTH_RS02650	SUTH_RS05575
Alternative steps:
ackA	acetate kinase	SUTH_RS02745	SUTH_RS10370
acs	acetyl-CoA synthetase, AMP-forming	SUTH_RS11485	SUTH_RS14820
adh	acetaldehyde dehydrogenase (not acylating)	SUTH_RS08615	SUTH_RS05840
ald-dh-CoA	acetaldehyde dehydrogenase, acylating
badH	2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase	SUTH_RS08230	SUTH_RS10940
badI	2-ketocyclohexanecarboxyl-CoA hydrolase	SUTH_RS08545	SUTH_RS15075
badK	cyclohex-1-ene-1-carboxyl-CoA hydratase	SUTH_RS15075	SUTH_RS13975
bamB	class II benzoyl-CoA reductase, BamB subunit
bamC	class II benzoyl-CoA reductase, BamC subunit
bamD	class II benzoyl-CoA reductase, BamD subunit
bamE	class II benzoyl-CoA reductase, BamE subunit
bamF	class II benzoyl-CoA reductase, BamF subunit	SUTH_RS13775
bamG	class II benzoyl-CoA reductase, BamG subunit
bamH	class II benzoyl-CoA reductase, BamH subunit	SUTH_RS06865	SUTH_RS10170
bamI	class II benzoyl-CoA reductase, BamI subunit	SUTH_RS06870	SUTH_RS10175
boxA	benzoyl-CoA epoxidase, subunit A	SUTH_RS08150
boxB	benzoyl-CoA epoxidase, subunit B	SUTH_RS08155
boxC	2,3-epoxybenzoyl-CoA dihydrolase	SUTH_RS08160
boxD	3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
catI	3-oxoadipate CoA-transferase subunit A (CatI)
catJ	3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA	cyclohex-1-ene-1-carbonyl-CoA dehydrogenase	SUTH_RS02660	SUTH_RS02630
fcbT1	tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1
fcbT2	tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2
fcbT3	tripartite 4-hydroxybenzoate transporter, large permease subunit FcbT3	SUTH_RS17660	SUTH_RS06085
ligA	protocatechuate 4,5-dioxygenase, alpha subunit	SUTH_RS06170	SUTH_RS06190
ligB	protocatechuate 4,5-dioxygenase, beta subunit	SUTH_RS06175	SUTH_RS06195
ligC	2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase	SUTH_RS06180
ligI	2-pyrone-4,6-dicarboxylate hydrolase	SUTH_RS06165
ligJ	4-carboxy-2-hydroxymuconate hydratase	SUTH_RS06150
ligK	4-oxalocitramalate aldolase	SUTH_RS06155	SUTH_RS05390
ligU	4-oxalomesaconate tautomerase
mhpD	2-hydroxypentadienoate hydratase
mhpE	4-hydroxy-2-oxovalerate aldolase	SUTH_RS08605	SUTH_RS16720
paaF	2,3-dehydroadipyl-CoA hydratase	SUTH_RS15075	SUTH_RS10290
paaH	3-hydroxyadipyl-CoA dehydrogenase	SUTH_RS07375	SUTH_RS03100
paaJ2	3-oxoadipyl-CoA thiolase	SUTH_RS13985	SUTH_RS01990
pcaB	3-carboxymuconate cycloisomerase
pcaC	4-carboxymuconolactone decarboxylase	SUTH_RS16040
pcaD	3-oxoadipate enol-lactone hydrolase	SUTH_RS16040
pcaF	succinyl-CoA:acetyl-CoA C-succinyltransferase	SUTH_RS13985	SUTH_RS01990
pcaG	protocatechuate 3,4-dioxygenase, beta subunit
pcaH	protocatechuate 3,4-dioxygenase, alpha subunit
pcaI	3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ	3-oxoadipate CoA-transferase subunit B (PcaJ)
pimC	pimeloyl-CoA dehydrogenase, small subunit	SUTH_RS11550	SUTH_RS11645
pimD	pimeloyl-CoA dehydrogenase, large subunit	SUTH_RS11545	SUTH_RS11640
pimF	6-carboxyhex-2-enoyl-CoA hydratase	SUTH_RS05635	SUTH_RS00440
pobA	4-hydroxybenzoate 3-monooxygenase	SUTH_RS06200
praA	protocatechuate 2,3-dioxygenase
praB	2-hydroxymuconate 6-semialdehyde dehydrogenase	SUTH_RS08615	SUTH_RS05840
praC	2-hydroxymuconate tautomerase
praD	2-oxohex-3-enedioate decarboxylase
pta	phosphate acetyltransferase	SUTH_RS10365	SUTH_RS14935
xylF	2-hydroxymuconate semialdehyde hydrolase

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.