L-lysine biosynthesis by the succinylated diaminopimelate pathway

Bacterial L-lysine biosynthesis from L-aspartate 4-semialdehyde and pyruvate through the succinylated diaminopimelate route. DapA and DapB form and reduce the tetrahydrodipicolinate intermediate. DapD masks it by succinylation, DapC introduces the second amino group, and DapE removes the succinyl group. DapF converts LL-diaminopimelate to meso-diaminopimelate, and LysA performs the terminal decarboxylation to L-lysine. Aspartate kinase and aspartate-semialdehyde dehydrogenase provide a shared precursor used by lysine, threonine, and methionine synthesis and are outside the dedicated module boundary. The meso-diaminopimelate product also feeds peptidoglycan assembly before its conversion to lysine.

MODULE:lysine_biosynthesisDRAFTMetabolic Pathwaymodules/lysine_biosynthesis.yaml
L-lysine biosynthetic processGO:0009085
GO:0009085
L-lysine biosynthetic process
The module is grounded in the current GO biological-process term for L-lysine biosynthesis.
KEGG:ppu00300
Pseudomonas putida KT2440 lysine biosynthesis
The PSEPK pathway instance supplies candidate proteins for the succinylated DAP route together with upstream, peptidoglycan, and paralogous map members that require boundary curation.
UniPathway:UPA00034
L-lysine biosynthesis via the diaminopimelate pathway
UniPathway grounds the DapA, DapB, DapD, DapC, DapE, DapF, and LysA reaction sequence represented here.
file:projects/P_PUTIDA/data/psepk_gene_list.tsv
PSEPK UniProt metadata table
Supplies exact PSEPK accessions, locus tags, pathway assignments, and family identifiers for the representative members.
file:projects/P_PUTIDA/deep-research/PSEPK__lysine_biosynthesis__ppu00300-deep-research-openscientist.md
OpenScientist module/pathway/taxon report for PSEPK L-lysine biosynthesis
Supports a complete seven-reaction succinylated-DAP route in KT2440 and the dedicated DapC family assignment for PP_1588. The report found no target-strain enzyme assays and treats physiological use of the DapA, DapF, and LysA paralogs as unresolved; sequence-identity rankings alone are not used here to discard exact UniProt-supported copies.
PMID:40774471
Cofactor-Independent Amino Acid Epimerases with Catalytic Serines Instead of Cysteines
Establishes a paired-serine DapF-SS class that catalyzes the same DAP epimerization as canonical paired-cysteine DapF-CC enzymes.
file:PSEPK/dapF__Q88GD4/dapF__Q88GD4-deep-research-openscientist.md
OpenScientist gene-level synthesis for PSEPK DapF Q88GD4
Maps Ser70 and Ser205 in Q88GD4 to the two canonical catalytic positions, supporting a putative DapF-SS assignment while noting that this exact protein has not been assayed.
8Nodes
7Parts
0Variant Sets
0Variants
7Annotons
6Connections

Derived QC

Recommended-field compliance

80.0% recommended fields populated
  • module.knowledge_gaps[0] · provenance (0/1)

Module deep research

✗ none found

No MODULE:lysine_biosynthesis 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.

  • dapA_step → dapB_step [NOT_CHECKED]
  • dapB_step → dapD_step [NOT_CHECKED]
  • dapD_step → dapC_step [NOT_CHECKED]
  • dapC_step → dapE_step [NOT_CHECKED]
  • dapE_step → dapF_step [NOT_CHECKED]
  • dapF_step → lysA_step [NOT_CHECKED]

Gene-review completeness (10/10 grounded genes reviewed)

10 complete review(s) · 8 with deep research · 0 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
dapA Q88JL0 ✓ ✓ ✗
dapA Q88NH2 ✓ ✓ ✓
dapB Q88DU4 ✓ ✓ ✗
dapC Q88MI3 ✓ ✓ ✓
dapD Q88MP1 ✓ ✓ ✓
dapE Q88MP5 ✓ ✓ ✓
dapF Q88CF3 ✓ ✓ ✓
dapF Q88GD4 ✓ ✓ ✓
lysA-I Q88L58 ✓ ✓ ✓
lysA-II Q88CF4 ✓ ✓ ✓

Details

succinylated diaminopimelate pathway of L-lysine biosynthesisMetabolic Pathwaylysine_biosynthesis
L-lysine biosynthetic processGO:0009085

PP_2036 is DapA-like but lacks the DapA-specific InterPro/HAMAP and lysine-pathway assignments present on Q88NH2 and Q88JL0, so it is not counted in this first-pass module. Aspartate kinase and Asd are shared upstream precursor-supply enzymes. MurE/MurF consume meso-diaminopimelate for peptidoglycan and are outside L-lysine formation. Broader aminotransferases are not substituted for the DapC-specific family without physiological evidence.

Connections

dapA_step -> dapB_step Precedes
dapB_step -> dapD_step Precedes
dapD_step -> dapC_step Precedes
dapC_step -> dapE_step Precedes
dapE_step -> dapF_step Precedes
dapF_step -> lysA_step Precedes
Part 1: committed diaminopimelate-ring formation
Aspartate semialdehyde and pyruvate to hydroxytetrahydrodipicolinateReactiondapA_step

Annotons

DapA hydroxytetrahydrodipicolinate synthase
dapA_activity
Participant: Family: DapA dihydrodipicolinate synthase family
Family:
DapA dihydrodipicolinate synthase familyInterPro:IPR005263
Representative Members: PSEPK DapA-IUniProtKB:Q88NH2 PSEPK DapA-IIUniProtKB:Q88JL0
Required Function:
4-hydroxy-tetrahydrodipicolinate synthase activityGO:0008840

Function

4-hydroxy-tetrahydrodipicolinate synthase activityGO:0008840
Substrates: L-aspartate 4-semialdehyde pyruvate
Products: (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate water

First pathway-specific reaction after the shared aspartate-semialdehyde precursor.

Part 2: tetrahydrodipicolinate reduction
Hydroxytetrahydrodipicolinate to tetrahydrodipicolinateReactiondapB_step

Annotons

DapB hydroxytetrahydrodipicolinate reductase
dapB_activity
Participant: Family: bacterial DapB family
Family:
bacterial DapB familyNCBIfam:TIGR00036
Representative Members: PSEPK DapBUniProtKB:Q88DU4
Required Function:
4-hydroxy-tetrahydrodipicolinate reductase activityGO:0008839

Function

4-hydroxy-tetrahydrodipicolinate reductase activityGO:0008839
Substrates: (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate NADPH or NADH
Products: (S)-2,3,4,5-tetrahydrodipicolinate NADP+ or NAD+
Part 3: tetrahydrodipicolinate succinylation
Tetrahydrodipicolinate to N-succinyltetrahydrodipicolinateReactiondapD_step

Annotons

DapD tetrahydrodipicolinate N-succinyltransferase
dapD_activity
Participant: Family: gammaproteobacterial DapD family
Family:
gammaproteobacterial DapD familyNCBIfam:TIGR03536
Representative Members: PSEPK DapDUniProtKB:Q88MP1
Required Function:
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activityGO:0008666

Function

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activityGO:0008666
Substrates: (S)-2,3,4,5-tetrahydrodipicolinate succinyl-CoA
Products: N-succinyl-2-amino-6-oxopimelate coenzyme A
Part 4: succinyldiaminopimelate transamination
N-succinyl-2-amino-6-oxopimelate to N-succinyl-LL-diaminopimelateReactiondapC_step

Annotons

DapC succinyldiaminopimelate aminotransferase
dapC_activity
Participant: Family: beta/gammaproteobacterial DapC family
Family:
beta/gammaproteobacterial DapC familyNCBIfam:TIGR03538
Representative Members: PSEPK DapCUniProtKB:Q88MI3
Required Function:
succinyldiaminopimelate:2-oxoglutarate transaminase activityGO:0009016

Function

succinyldiaminopimelate:2-oxoglutarate transaminase activityGO:0009016
Substrates: N-succinyl-2-amino-6-oxopimelate L-glutamate
Products: N-succinyl-LL-2,6-diaminopimelate 2-oxoglutarate
Cofactors: pyridoxal 5'-phosphate
Part 5: LL-diaminopimelate deprotection
N-succinyl-LL-diaminopimelate to LL-diaminopimelateReactiondapE_step

Annotons

DapE succinyl-diaminopimelate desuccinylase
dapE_activity
Participant: Family: proteobacterial DapE family
Family:
proteobacterial DapE familyNCBIfam:TIGR01246
Representative Members: PSEPK DapEUniProtKB:Q88MP5
Required Function:
succinyl-diaminopimelate desuccinylase activityGO:0009014

Function

succinyl-diaminopimelate desuccinylase activityGO:0009014
Substrates: N-succinyl-LL-2,6-diaminopimelate water
Products: LL-2,6-diaminopimelate succinate
Cofactors: two zinc or cobalt ions
Part 6: meso-diaminopimelate formation
LL-diaminopimelate to meso-diaminopimelateReactiondapF_step

Annotons

DapF diaminopimelate epimerase
dapF_activity
Participant: Family: DapF diaminopimelate epimerase family
Family:
DapF diaminopimelate epimerase familyNCBIfam:TIGR00652
Representative Members: PSEPK DapF-IUniProtKB:Q88GD4 PSEPK DapF-IIUniProtKB:Q88CF3
Required Function:
diaminopimelate epimerase activityGO:0008837

Function

diaminopimelate epimerase activityGO:0008837
Substrates: LL-2,6-diaminopimelate
Products: meso-2,6-diaminopimelate

Produces meso-diaminopimelate, which is both the LysA substrate and a peptidoglycan precursor.

Part 7: terminal L-lysine formation
meso-Diaminopimelate to L-lysineReactionlysA_step

Annotons

LysA diaminopimelate decarboxylase
lysA_activity
Participant: Family: LysA diaminopimelate decarboxylase family
Family:
LysA diaminopimelate decarboxylase familyNCBIfam:TIGR01048
Representative Members: PSEPK LysA-IUniProtKB:Q88L58 PSEPK LysA-IIUniProtKB:Q88CF4
Required Function:
diaminopimelate decarboxylase activityGO:0008836

Function

diaminopimelate decarboxylase activityGO:0008836
Substrates: meso-2,6-diaminopimelate
Products: L-lysine carbon dioxide
Cofactors: pyridoxal 5'-phosphate