L-arginine catabolism in Rhodococcus qingshengii djl-6-2

Best path

bgtB, artP, arg-monooxygenase, gbamidase, kauB, gbuA, gabT, gabD

Rules

Overview: Arginine utilization in GapMind is based on MetaCyc pathways L-arginine degradation I via arginase (link); II via arginine succinyltransferase (link), III via arginine decarboxylase and agmatinase (link), IV via arginine decarboxylase and agmatine deiminase (link), V via arginine deiminase (link), VI (arginase 2, link), VII (arginase 3, link), VIII via arginase oxidase (link), IX via arginine:pyruvate transaminase (link), X via arginine monooxygenase (link), XIII via proline (link), and XIV via D-ornithine (link). Common intermediates are L-ornithine or L-proline. GapMind does not include pathways XI (link), which is poorly understood, or XII (link), which is not reported in prokaryotes.

• all:
  • arginine-transport, rocF and ornithine-degradation
  • or arginine-transport, arginine-succinyltransferase, astB, astC, astD and astE
  • or arginine-transport, adiA, speB and putrescine-degradation
  • or arginine-transport, adiA, aguA, aguB and putrescine-degradation
  • or arginine-transport, arcA, arcB, arcC and ornithine-degradation
  • or arginine-transport, aroD, aruI, kauB, gbuA and GABA-degradation
  • or arginine-transport, aruH, aruI, kauB, gbuA and GABA-degradation
  • or arginine-transport, arg-monooxygenase, gbamidase, kauB, gbuA and GABA-degradation
  • Comment: Pathways I, VI, or VII begin with rocF (arginase), which forms ornithine and urea. (The urea might not be utilized, so urease is not described here.) They differ in how the ornithine is catabolized. Pathway II begins with arginine succinyltransferase and ends with succinate and glutamate. The succinate would then be activated to succinyl-CoA to restart the cycle, or the glutamate might be oxidized to succinyl-CoA; these steps are not included here. Pathway III begins with decarboxylation to agmatine by adiA, followed by hydrolysis to putrescine and urea. Pathway IV begins with adiA and agmatine deiminase (aguA), which yields N-carbamoylputrescine; this is hydrolyzed to putrescine and urea. Pathway V begins with arginine deiminase (arcA), forming citrulline, and and a carbamoyltransferase forms carbamoyl-phosphate and ornithine. The carbamoyl-phosphate is consumed by carbamate kinase (in reverse, forming ammonia and CO2 and ATP). Pathway VIII begins with arginine oxidase aroD, which forms 5-guanidino-2-oxopentanoate (2-ketoarginine); this is converted to gamma-aminobutyrate (GABA). Pathway IX is similar to pathway VIII but the transaminase aruH forms the 5-guanidino-2-oxopentanoate. Pathway X involves arginine 2-monooxygenase (decarboxylating), forming 4-guanidinobutyramide, and an amidase, forming 4-guanidinobutyrate, which is consumed as in pathway VIII or IX.
• ornithine-degradation:
  • aruF, aruG, astC, astD and astE
  • or rocD and rocA
  • or rocD, PRO3 and proline-degradation
  • or ocd and proline-degradation
  • or odc and putrescine-degradation
  • or orr, oraS, oraE, ord, ortA and ortB
  • Comment: Ornithine is a common intermediate. It can be succinylated by aruFG and then catabolized by the later steps of the arginine succinyltransferase pathway, via aminotransferase, dehydrogenase, and desuccinylase reactions (see PMC179677 and PMID:7523119). Or as part of L-arginine degradation I, the aminotransferase rocD converts ornithine to glutamate 5-semialdehyde, which spontaneously converts to 1-pyrroline-5-carboxylate. A dehydrogenase converts this to glutamate. Or 1-pyrroline-5-carboxylate can be reduced to proline by PRO3, as in L-arginine degradation VI. Alternatively, ornithine can be converted directly to proline by ornithine cyclodeaminase (ocd). Or ornithine can be decarboxylated to putrescine by odc (link). Or ornithine can be catabolized via D-ornithine, as in L-arginine degradation XIV. A racemase converts L-ornithine to D-ornithine; an aminomutase forms (2R,4S) 2,4-diaminopentanoate; a dehydrogenase forms (2R)-2-amino-4-oxopentanoate, and a thiolase cleaves it to D-alanine and acetyl-CoA. D-alanine could be oxidized to pyruvate or perhaps secreted; this is not described here.
• arginine-succinyltransferase:
  • aruF and aruG
  • or astA
• proline-degradation:
  • put1 and putA
  • or prdF, D-proline-reductase and 5-aminovalerate-degradation
  • Comment: In pathway I, proline dehydrogenase (put1) forms (S)-1-pyrroline-5-carboxylate, which spontaneously hydrates to L-glutamate 5-semialdehyde, and a dehydrogenase (putA) to glutamate. Glutamate can be transaminated to 2-oxoglutarate, which is an intermediate in central metabolism (not represented). In pathway II, proline racemase (prdF) forms D-proline, and a reductase forms 5-aminovalerate.
• D-proline-reductase: prdA, prdB and prdC
  • Comment: D-proline reductase includes components PrdA and PrdB and electron transfer protein PrdC
• 5-aminovalerate-degradation: davT, davD and glutarate-degradation
  • Comment: 5-aminovalerate is an intermediate in L-lysine degradation (link, link). It is transaminated to glutarate semialdehyde and oxidized to glutarate. (A fermentative pathway via 5-hydroxyvalerate has also been reported, but does not seem to be fully linked to sequence; see pathway 5 of PMID:11759672.)
• glutarate-degradation:
  • glaH and lhgD
  • or gcdG and glutaryl-CoA-degradation
  • Comment: Glutarate is an intermediate in L-lysine degradation. As part of MetaCyc pathway L-lysine degradation I (link), gluratate is hydroxylated to L-2-hydroxyglutarate (also known as (S)-2-hydroxyglutarate) by a 2-oxoglutarate-dependent oxidase. This reaction releases succinate (a TCA cycle intermediate) and CO2. A dehydrogenase then oxidizes to L-2-hydroxyglutarate to regenerate 2-oxoglutarate. Alternatively, as part of pathway IV (link), glutarate can be activated to glutaryl-CoA by a CoA-transferase. Glutaryl-CoA degradation (link) involves glutaryl-CoA dehydrogenase (decarboxylating) to crotonyl-CoA (trans-but-2-enoyl-CoA), hydration to (S)-hydroxybutanoyl-CoA, oxidization to acetoacetyl-CoA, and cleavage by a C-acetyltransferase to two acetyl-CoA.
• 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.
• GABA-degradation: gabT and gabD
  • Comment: GABA (4-aminobutanoate) is consumed by an aminotransferase (known as gabT or puuE), which forms succinate semialdehyde, and dehydrogenase gabD, which forms succinate.
• putrescine-degradation: putrescine-to-GABA and GABA-degradation
  • Comment: Gamma-aminobutyrate is a common intermediate.
• putrescine-to-GABA:
  • patA and patD
  • or puuA, puuB, puuC and puuD
  • or puo and patD
  • Comment: In pathway I or pathway V, putrescine aminotransferase (patA or spuC) forms 4-aminobutanal, and dehydrogenase patD forms GABA. In pathway II, putrescine is converted to GABA with glutamylated intermedates: puuA forms gamma-glutamyl-putrescine, an oxidase forms 4-(gamma-glutaminylamino)butanal, a dehydrogenase forms 4-(gamma-glutamylamino)butanoate, and a hydrolase releases glutamate and GABA. As part of pathway IV, putrescine oxidase (puo) forms 4-aminobutanal, which is probably converted to GABA by dehydrogenase patD.
• arginine-transport:
  • artJ, artM, artP and artQ
  • or bgtB and artP
  • or braC, braD, braE, braF and braG
  • or rocE
  • or AAP3
  • or CAT1
  • or Can1
  • Comment: Transporters were identified using: query: transporter:arginine:L-arginine:arg.

71 steps (46 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
bgtB	L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)	C1M55_RS30350	C1M55_RS21980
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	C1M55_RS21985	C1M55_RS16555
arg-monooxygenase	arginine 2-monooxygenase	C1M55_RS03275
gbamidase	guanidinobutyramidase	C1M55_RS03270
kauB	4-guanidinobutyraldehyde dehydrogenase	C1M55_RS09205	C1M55_RS09155
gbuA	guanidinobutyrase	C1M55_RS03260
gabT	gamma-aminobutyrate transaminase	C1M55_RS14045	C1M55_RS30115
gabD	succinate semialdehyde dehydrogenase	C1M55_RS00485	C1M55_RS22335
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)
aguA	agmatine deiminase	C1M55_RS22245	C1M55_RS28980
aguB	N-carbamoylputrescine hydrolase	C1M55_RS22240
arcA	arginine deiminase	C1M55_RS22045
arcB	ornithine carbamoyltransferase	C1M55_RS16385	C1M55_RS14945
arcC	carbamate kinase
aroD	L-arginine oxidase
artJ	L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT	C1M55_RS16565	C1M55_RS21980
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	C1M55_RS21980	C1M55_RS16560
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	C1M55_RS21980	C1M55_RS07370
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH	L-arginine:pyruvate transaminase	C1M55_RS23515	C1M55_RS01535
aruI	2-ketoarginine decarboxylase	C1M55_RS12505
astA	arginine N-succinyltransferase
astB	N-succinylarginine dihydrolase
astC	succinylornithine transaminase	C1M55_RS16390	C1M55_RS28045
astD	succinylglutamate semialdehyde dehydrogenase	C1M55_RS28050	C1M55_RS27350
astE	succinylglutamate desuccinylase
atoB	acetyl-CoA C-acetyltransferase	C1M55_RS28700	C1M55_RS07210
braC	ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	C1M55_RS06865
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	C1M55_RS16605	C1M55_RS22585
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	C1M55_RS22600	C1M55_RS08560
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	C1M55_RS06875	C1M55_RS22595
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1	C1M55_RS10990	C1M55_RS12490
davD	glutarate semialdehyde dehydrogenase	C1M55_RS22335	C1M55_RS03295
davT	5-aminovalerate aminotransferase	C1M55_RS28045	C1M55_RS03290
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	C1M55_RS19610	C1M55_RS12340
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	C1M55_RS07980	C1M55_RS25285
gcdG	succinyl-CoA:glutarate CoA-transferase	C1M55_RS24685	C1M55_RS30270
gcdH	glutaryl-CoA dehydrogenase	C1M55_RS24690	C1M55_RS09530
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd	ornithine cyclodeaminase
odc	L-ornithine decarboxylase
oraE	D-ornithine 4,5-aminomutase, beta (E) subunit
oraS	D-ornithine 4,5-aminomutase, alpha (S) subunit
ord	2,4-diaminopentanoate dehydrogenase
orr	ornithine racemase	C1M55_RS20010
ortA	2-amino-4-oxopentanoate thiolase, alpha subunit
ortB	2-amino-4-oxopentanoate thiolase, beta subunit
patA	putrescine aminotransferase (PatA/SpuC)	C1M55_RS30115	C1M55_RS14045
patD	gamma-aminobutyraldehyde dehydrogenase	C1M55_RS22220	C1M55_RS28575
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase
PRO3	pyrroline-5-carboxylate reductase	C1M55_RS08270
puo	putrescine oxidase	C1M55_RS22210
put1	proline dehydrogenase	C1M55_RS23685	C1M55_RS23680
putA	L-glutamate 5-semialdeyde dehydrogenase	C1M55_RS23680	C1M55_RS02975
puuA	glutamate-putrescine ligase	C1M55_RS30570	C1M55_RS17840
puuB	gamma-glutamylputrescine oxidase
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	C1M55_RS09205	C1M55_RS09155
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	C1M55_RS30560
rocA	1-pyrroline-5-carboxylate dehydrogenase	C1M55_RS23680	C1M55_RS02975
rocD	ornithine aminotransferase	C1M55_RS03290	C1M55_RS28045
rocE	L-arginine permease	C1M55_RS01060	C1M55_RS07700
rocF	arginase	C1M55_RS03260	C1M55_RS25930
speB	agmatinase	C1M55_RS03260

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.