Bacterial succinylarginine catabolism to glutamate and succinate

A five-reaction bacterial pathway that transfers a succinyl group from succinyl-CoA to L-arginine, hydrolyzes the guanidino group, transaminates the resulting N-succinyl-L-ornithine, oxidizes the semialdehyde, and removes the succinyl group to produce L-glutamate and succinate. The initiating transferase may be a single-chain enzyme or a two-chain complex. Arginine transport, regulation, alternative arginine-catabolic routes, and downstream central metabolism are outside the module boundary.

MODULE:bacterial_succinylarginine_catabolismDRAFTCONCRETEMetabolic Pathwaymodules/bacterial_succinylarginine_catabolism.yaml
L-arginine catabolic processGO:0006527
PMID:2865249
Occurrence of succinyl derivatives in the catabolism of arginine in Pseudomonas cepacia.
Defines the ordered five-reaction pathway from arginine through succinylated intermediates to glutamate and succinate.
PMID:7523119
Purification and properties of a succinyltransferase from Pseudomonas aeruginosa specific for both arginine and ornithine.
Establishes a two-chain heterotetrameric Pseudomonas implementation of the initiating transferase.
PMID:9393691
Cloning and characterization of the aru genes encoding enzymes of the catabolic arginine succinyltransferase pathway in Pseudomonas aeruginosa.
Assigns the two AstA chains and the four downstream enzyme roles in a Pseudomonas AST pathway.
PMID:23484010
Determination of the structure of the catabolic N-succinylornithine transaminase (AstC) from Escherichia coli.
Establishes the PLP-dependent AstC reaction with succinylornithine and 2-oxoglutarate.
file:PSEPK/argD/argD-deep-research-openscientist.md
OpenScientist synthesis for PSEPK PP_4481 acyl-ornithine aminotransferase
Integrates KT2440 locus context, PANTHER subfamily placement, and comparative literature to identify PP_4481 as the pathway's AstC-like transaminase while retaining secondary acetylornithine activity as plausible.

The module is species-neutral. Pseudomonas putida KT2440 proteins are included as concrete representatives, not as a restriction on taxonomic scope. Exact UniProt identities and PANTHER assignments were checked against current UniProt records. GOA WITH/FROM values PTN002279553 (P59319) and PTN002309601 (Q88EI7) were verified as the sources of broad PLP/self-binding and amide-hydrolase annotations, respectively. They are not used as ancestral nodes because the available evidence does not establish the exact substrate-specific AstC or AstE function at those nodes. InterPro IPR017651 and IPR017650, corroborated by NCBIfam TIGR03245 and TIGR03244, distinguish the alpha-like and beta-like components of split AstA, respectively; PANTHER PTHR30420:SF1 groups both chain types with single-chain AstA and therefore does not discriminate the architecture. The AstD selector uses broad PTHR11699 because the checked Q88EI4 and P76217 member records have no populated PANTHER subfamily.

8Nodes
5Parts
1Variant Sets
2Variants
6Annotons
4Connections

Derived QC

Recommended-field compliance

55.6% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)

Module deep research

✗ none found

No MODULE:bacterial_succinylarginine_catabolism deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • asta_arginine_succinylation → astb_succinylarginine_hydrolysis [NOT_CHECKED]
    The AstA product is the explicit AstB substrate.
  • astb_succinylarginine_hydrolysis → astc_succinylornithine_transamination [NOT_CHECKED]
    The AstB product is the explicit AstC substrate.
  • astc_succinylornithine_transamination → astd_semialdehyde_oxidation [NOT_CHECKED]
    The AstC product is the explicit AstD substrate.
  • astd_semialdehyde_oxidation → aste_desuccinylation [NOT_CHECKED]
    The AstD product is the explicit AstE substrate.

Gene-review completeness (6/14 grounded genes reviewed)

6 complete review(s) · 1 with deep research · 8 missing review · 5 reviewed but lacking deep research

Gene Review Complete Deep research
argD P59319 ✓ ✓ ✓
astA-I Q88EI3 ✓ ✓ ✗
astA-II Q88EI2 ✓ ✓ ✗
astB Q88EI5 ✓ ✓ ✗
astD Q88EI4 ✓ ✓ ✗
astE Q88EI7 ✓ ✓ ✗
Pseudomonas aeruginosa AruC O30508 ✗ — —
Escherichia coli AstA P0AE37 ✗ — —
Escherichia coli AstE P76215 ✗ — —
Escherichia coli AstB P76216 ✗ — —
Escherichia coli AstD P76217 ✗ — —
Escherichia coli AstC P77581 ✗ — —
Pseudomonas aeruginosa AruF P80357 ✗ — —
Pseudomonas aeruginosa AruG P80358 ✗ — —

Details

Context
bacteriaNCBITaxon:2
Bacterial succinylarginine catabolism to glutamate and succinateMetabolic Pathwaybacterial_succinylarginine_catabolism
L-arginine catabolic processGO:0006527
Context
bacteriaNCBITaxon:2

Connections

AstA supplies N-succinyl-L-arginine to AstB.
AstB supplies N-succinyl-L-ornithine to AstC.
AstC supplies N-succinyl-L-glutamate 5-semialdehyde to AstD.
AstD supplies N-succinyl-L-glutamate to AstE.
Part 1: arginine succinylation
L-arginine to N-succinyl-L-arginineReactionasta_arginine_succinylation
Variant set: AstA enzyme architecture variants by enzyme architecture (Exactly One)
Split-chain AstA complexReactionsplit_asta_variant

Annotons

Two-chain arginine N-succinyltransferase
split_asta_activity
Participant: Protein Complex: split-chain AstA arginine N-succinyltransferase
Protein Complex:
split-chain AstA arginine N-succinyltransferase Heterotetrameric Pseudomonas-type implementation with two alpha-like and two beta-like chains.
Active units:
AstA alpha-like chain
Participant: Family: AstA alpha-subunit family
Family:
AstA alpha-subunit familyInterPro:IPR017651
Representative Members: Pseudomonas aeruginosa AruFUniProtKB:P80357 Pseudomonas putida AstA-IIUniProtKB:Q88EI2
Role: Required alpha-like component of the split transferase.
AstA beta-like chain
Participant: Family: AstA beta-subunit family
Family:
AstA beta-subunit familyInterPro:IPR017650
Representative Members: Pseudomonas aeruginosa AruGUniProtKB:P80358 Pseudomonas putida AstA-IUniProtKB:Q88EI3
Role: Required beta-like component of the split transferase.
Required Function:
L-arginine N-succinyltransferase activityGO:0008791

Function

L-arginine N-succinyltransferase activityGO:0008791
Substrates: L-arginine succinyl-CoA
Products: N-succinyl-L-arginine CoA

Processes

L-arginine catabolic processGO:0006527
Single-chain AstA enzymeReactionsingle_chain_asta_variant

Annotons

Single-chain arginine N-succinyltransferase
single_chain_asta_activity
Participant: Family: single-chain AstA family
Family:
single-chain AstA familyPANTHER:PTHR30420:SF1
Representative Members: Escherichia coli AstAUniProtKB:P0AE37
Required Function:
L-arginine N-succinyltransferase activityGO:0008791

Function

L-arginine N-succinyltransferase activityGO:0008791
Substrates: L-arginine succinyl-CoA
Products: N-succinyl-L-arginine CoA

Processes

L-arginine catabolic processGO:0006527
Part 2: N-succinylarginine hydrolysis
N-succinyl-L-arginine to N-succinyl-L-ornithineReactionastb_succinylarginine_hydrolysis

Annotons

N-succinylarginine dihydrolase
astb_activity
Participant: Family: AstB N-succinylarginine dihydrolase family
Family:
AstB N-succinylarginine dihydrolase familyPANTHER:PTHR30420:SF2
Representative Members: Pseudomonas putida AstBUniProtKB:Q88EI5 Escherichia coli AstBUniProtKB:P76216
Required Function:
N-succinylarginine dihydrolase activityGO:0009015

Function

N-succinylarginine dihydrolase activityGO:0009015
Substrates: N-succinyl-L-arginine water
Products: N-succinyl-L-ornithine ammonium carbon dioxide

Processes

L-arginine catabolic processGO:0006527
Part 3: N-succinylornithine transamination
N-succinyl-L-ornithine transaminationReactionastc_succinylornithine_transamination

Annotons

Succinylornithine transaminase
astc_activity
Participant: Family: AstC succinylornithine transaminase subfamily
Family:
AstC succinylornithine transaminase subfamilyPANTHER:PTHR11986:SF113
Representative Members: Pseudomonas aeruginosa AruCUniProtKB:O30508 Escherichia coli AstCUniProtKB:P77581 Pseudomonas putida AstC candidateUniProtKB:P59319
Required Function:
succinylornithine:2-oxoglutarate transaminase activityGO:0043825

Function

succinylornithine:2-oxoglutarate transaminase activityGO:0043825
Substrates: N-succinyl-L-ornithine 2-oxoglutarate
Products: N-succinyl-L-glutamate 5-semialdehyde L-glutamate

Processes

L-arginine catabolic processGO:0006527
Part 4: semialdehyde oxidation
N-succinyl-L-glutamate 5-semialdehyde oxidationReactionastd_semialdehyde_oxidation

Annotons

N-succinylglutamate-semialdehyde dehydrogenase
astd_activity
Participant: Family: AstD aldehyde dehydrogenase family
Family:
AstD aldehyde dehydrogenase familyPANTHER:PTHR11699
Representative Members: Pseudomonas putida AstDUniProtKB:Q88EI4 Escherichia coli AstDUniProtKB:P76217
Required Function:
succinylglutamate-semialdehyde dehydrogenase activityGO:0043824

Function

succinylglutamate-semialdehyde dehydrogenase activityGO:0043824
Substrates: N-succinyl-L-glutamate 5-semialdehyde NAD+ water
Products: N-succinyl-L-glutamate NADH

Processes

L-arginine catabolic processGO:0006527
Part 5: terminal desuccinylation
N-succinyl-L-glutamate hydrolysisReactionaste_desuccinylation

Annotons

Succinylglutamate desuccinylase
aste_activity
Participant: Family: AstE succinylglutamate desuccinylase subfamily
Family:
AstE succinylglutamate desuccinylase subfamilyPANTHER:PTHR15162:SF7
Representative Members: Pseudomonas putida AstEUniProtKB:Q88EI7 Escherichia coli AstEUniProtKB:P76215
Required Function:
succinylglutamate desuccinylase activityGO:0009017

Function

succinylglutamate desuccinylase activityGO:0009017
Substrates: N-succinyl-L-glutamate water
Products: L-glutamate succinate

Processes

L-arginine catabolic processGO:0006527