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.
UniPathway:UPA00034
L-lysine biosynthesis via the diaminopimelate pathway
UniPathway grounds the DapA, DapB, DapD, DapC, DapE, DapF, and LysA reaction sequence represented here.
KEGG:M00016
Lysine biosynthesis, succinyl-DAP pathway, aspartate => lysine
The species-neutral KEGG module independently defines the succinyl-DAP route and its DapA-through-LysA reaction sequence.
8Nodes
7Parts
0Variant Sets
0Variants
7Annotons
6Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

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]

Function consistency and core coverage

1 gene-function check(s) reflected in core functions · 0 conflict(s) · 15 evidence or coverage gap(s) (16 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
dapA_activity E. coli DapA
UniProtKB:P0A6L2
Family Representative 		4-hydroxy-tetrahydrodipicolinate synthase activity
GO:0008840 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dapB_activity E. coli DapB
UniProtKB:P04036
Family Representative 		4-hydroxy-tetrahydrodipicolinate reductase activity
GO:0008839 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dapD_activity E. coli DapD
UniProtKB:P0A9D8
Family Representative 		2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
GO:0008666 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dapC_activity Pseudomonas putida KT2440 DapC
UniProtKB:Q88MI3
Family Representative 		succinyldiaminopimelate:2-oxoglutarate transaminase activity
GO:0009016 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dapE_activity E. coli DapE
UniProtKB:P0AED7
Family Representative 		succinyl-diaminopimelate desuccinylase activity
GO:0009014 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dapF_activity E. coli DapF
UniProtKB:P0A6K1
Family Representative 		diaminopimelate epimerase activity
GO:0008837 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
lysA_activity E. coli LysA
UniProtKB:P00861
Family Representative 		diaminopimelate decarboxylase activity
GO:0008836 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dapA_activity DapA dihydrodipicolinate synthase family
PANTHER:PTHR12128
Family 		4-hydroxy-tetrahydrodipicolinate synthase activity
GO:0008840 		Family Scope Restricted
GO:0008840 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. DHDPS activity belongs to the bacterial DapA members of SF66 and to the plant chloroplastic enzymes of SF15 and SF71. It does not apply to the KDGDH (SF19), Pyr4H2C deaminase (SF72), NPL (SF21) or YagE/YjhH (SF28) lineages. Within SF66, the bilaterian HOGA1 aldolases are excepted, as the PAINT IRD at PTN000950946 records.
dapA_activity DapA dihydrodipicolinate synthase family
InterPro:IPR005263
Family 		4-hydroxy-tetrahydrodipicolinate synthase activity
GO:0008840 		Family Review Missing
No supported structured family review is available for InterPro:IPR005263.
dapB_activity bacterial DapB family
PANTHER:PTHR20836
Family 		4-hydroxy-tetrahydrodipicolinate reductase activity
GO:0008839 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR20836.
dapD_activity tetrahydrodipicolinate N-succinyltransferase family
NCBIfam:TIGR03536
Family 		2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
GO:0008666 		Family Review Missing
No supported structured family review is available for NCBIfam:TIGR03536.
dapC_activity dedicated beta/gammaproteobacterial DapC family
NCBIfam:TIGR03538
Family 		succinyldiaminopimelate:2-oxoglutarate transaminase activity
GO:0009016 		Family Review Missing
No supported structured family review is available for NCBIfam:TIGR03538.
dapC_activity dedicated beta/gammaproteobacterial DapC family
InterPro:IPR019878
Family 		succinyldiaminopimelate:2-oxoglutarate transaminase activity
GO:0009016 		Family Review Missing
No supported structured family review is available for InterPro:IPR019878.
dapE_activity succinyl-diaminopimelate desuccinylase family
NCBIfam:TIGR01246
Family 		succinyl-diaminopimelate desuccinylase activity
GO:0009014 		Family Review Missing
No supported structured family review is available for NCBIfam:TIGR01246.
dapF_activity DapF diaminopimelate epimerase family
PANTHER:PTHR31689
Family 		diaminopimelate epimerase activity
GO:0008837 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31689.
lysA_activity LysA diaminopimelate decarboxylase family
PANTHER:PTHR43727
Family 		diaminopimelate decarboxylase activity
GO:0008836 		Family Scope Restricted
GO:0008836 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. Safe for the LysA subfamily SF2 only. Tested SF1 representatives lack detectable activity on meso-diaminopimelate, so the term must not be inherited there, whether by IBA from PTN000159906 or by any other transfer.

Gene-review completeness (1/7 grounded genes reviewed)

1 complete review(s) · 1 with deep research · 6 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
dapC Q88MI3 ✓ ✓ ✓
E. coli LysA P00861 ✗ — —
E. coli DapB P04036 ✗ — —
E. coli DapF P0A6K1 ✗ — —
E. coli DapA P0A6L2 ✗ — —
E. coli DapD P0A9D8 ✗ — —
E. coli DapE P0AED7 ✗ — —

Details

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

The boundary begins at the first pathway-specific condensation and ends at L-lysine formation. Aspartate-semialdehyde supply is shared with other aspartate-family amino-acid pathways, while meso-diaminopimelate use in peptidoglycan is a downstream branch. The succinylated route is defined by the DapD, DapC, and DapE reactions; other taxonomic DAP-pathway variants are separate implementations.

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 familyPANTHER:PTHR12128 PTHR12128 is a broad parent spanning multiple aldolase subfamilies. The required GO:0008840 function and reviewed P0A6L2 reaction exemplar constrain this leaf, while InterPro IPR005263 supplies a DapA-specific family grounding; no misleading PANTHER subfamily identifier is asserted.
Representative Members: E. coli DapAUniProtKB:P0A6L2
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 familyPANTHER:PTHR20836
Representative Members: E. coli DapBUniProtKB:P04036
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-succinyl-2-amino-6-oxopimelateReactiondapD_step

Annotons

DapD tetrahydrodipicolinate N-succinyltransferase
dapD_activity
Participant: Family: tetrahydrodipicolinate N-succinyltransferase family
Family:
tetrahydrodipicolinate N-succinyltransferase familyNCBIfam:TIGR03536 TIGR03536 grounds the gamma-proteobacterial DapD implementation represented here; it is not intended to exhaust the taxonomic breadth of enzymes that perform the required GO:0008666 reaction.
Representative Members: E. coli DapDUniProtKB:P0A9D8
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 water
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: dedicated beta/gammaproteobacterial DapC family
Family:
dedicated beta/gammaproteobacterial DapC family TIGR03538 and IPR019878 describe the dedicated beta/gammaproteobacterial DapC implementation. Other lineages can fill the same required reaction with a distinct enzyme, including bifunctional ArgD proteins.
Representative Members: Pseudomonas putida KT2440 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: succinyl-diaminopimelate desuccinylase family
Family:
succinyl-diaminopimelate desuccinylase familyNCBIfam:TIGR01246 TIGR01246 grounds a proteobacterial DapE implementation; the required GO:0009014 reaction, rather than this lineage-limited equivalog alone, defines the reusable module step.
Representative Members: E. coli DapEUniProtKB:P0AED7
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 familyPANTHER:PTHR31689 The official PTHR31689 parent label is chloroplast-biased, but the family contains reviewed bacterial DapF proteins, including P0A6K1, and the exact PAINT node below carries the bacterial diaminopimelate epimerase activity.
Representative Members: E. coli DapFUniProtKB:P0A6K1
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 familyPANTHER:PTHR43727
Representative Members: E. coli LysAUniProtKB:P00861
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