L-arginine catabolism in Brevibacterium jeotgali SJ5-8

Best path

bgtB, artP, aruH, aruI, 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 (37 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)
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	BJEO58_RS10155	BJEO58_RS06850
aruH	L-arginine:pyruvate transaminase	BJEO58_RS07370	BJEO58_RS10030
aruI	2-ketoarginine decarboxylase	BJEO58_RS08980	BJEO58_RS03915
kauB	4-guanidinobutyraldehyde dehydrogenase	BJEO58_RS09005	BJEO58_RS05335
gbuA	guanidinobutyrase	BJEO58_RS08975
gabT	gamma-aminobutyrate transaminase	BJEO58_RS06635	BJEO58_RS05345
gabD	succinate semialdehyde dehydrogenase	BJEO58_RS06110	BJEO58_RS08335
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)
aguA	agmatine deiminase
aguB	N-carbamoylputrescine hydrolase	BJEO58_RS07845
arcA	arginine deiminase
arcB	ornithine carbamoyltransferase	BJEO58_RS04775	BJEO58_RS02790
arcC	carbamate kinase
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
artJ	L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	BJEO58_RS10145	BJEO58_RS10150
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	BJEO58_RS10150	BJEO58_RS04215
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astA	arginine N-succinyltransferase
astB	N-succinylarginine dihydrolase
astC	succinylornithine transaminase	BJEO58_RS04770	BJEO58_RS06635
astD	succinylglutamate semialdehyde dehydrogenase	BJEO58_RS05335	BJEO58_RS11450
astE	succinylglutamate desuccinylase
atoB	acetyl-CoA C-acetyltransferase	BJEO58_RS06055	BJEO58_RS05920
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)
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	BJEO58_RS03195	BJEO58_RS05330
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	BJEO58_RS06110	BJEO58_RS12670
davT	5-aminovalerate aminotransferase	BJEO58_RS06635	BJEO58_RS06895
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	BJEO58_RS08900	BJEO58_RS03580
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	BJEO58_RS02050	BJEO58_RS13310
gbamidase	guanidinobutyramidase
gcdG	succinyl-CoA:glutarate CoA-transferase	BJEO58_RS08090	BJEO58_RS01755
gcdH	glutaryl-CoA dehydrogenase	BJEO58_RS04410	BJEO58_RS08890
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	BJEO58_RS05590
ocd	ornithine cyclodeaminase	BJEO58_RS07490
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
ortA	2-amino-4-oxopentanoate thiolase, alpha subunit
ortB	2-amino-4-oxopentanoate thiolase, beta subunit
patA	putrescine aminotransferase (PatA/SpuC)	BJEO58_RS05345	BJEO58_RS07400
patD	gamma-aminobutyraldehyde dehydrogenase	BJEO58_RS05335	BJEO58_RS12670
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	BJEO58_RS00590
puo	putrescine oxidase	BJEO58_RS09335
put1	proline dehydrogenase	BJEO58_RS03425
putA	L-glutamate 5-semialdeyde dehydrogenase	BJEO58_RS06985	BJEO58_RS13455
puuA	glutamate-putrescine ligase	BJEO58_RS13465	BJEO58_RS13725
puuB	gamma-glutamylputrescine oxidase
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	BJEO58_RS09005	BJEO58_RS05335
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	BJEO58_RS13460
rocA	1-pyrroline-5-carboxylate dehydrogenase	BJEO58_RS06985	BJEO58_RS13455
rocD	ornithine aminotransferase	BJEO58_RS06635	BJEO58_RS07400
rocE	L-arginine permease	BJEO58_RS06510
rocF	arginase	BJEO58_RS08975
speB	agmatinase	BJEO58_RS08975

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.