D-amino-acid supply for peptidoglycan precursor biosynthesis

A reusable bacterial precursor-supply module that produces D-glutamate and D-alanine from their L-enantiomers and ligates two D-alanine molecules to form D-Ala-D-Ala. These products feed the cytoplasmic Mur ligase pathway for peptidoglycan stem-peptide assembly. The module ends at free D-glutamate and D-Ala-D-Ala and excludes their incorporation by MurD and MurF, downstream lipid II synthesis, polymerization, cross-linking, D-amino-acid catabolism, periplasmic BSR metabolism, and Ldt-mediated peptidoglycan remodeling.

MODULE:d_amino_acid_cell_wall_precursor_supplyDRAFTMetabolic Pathwaymodules/d_amino_acid_cell_wall_precursor_supply.yaml
peptidoglycan biosynthetic processGO:0009252
GO:0009252
peptidoglycan biosynthetic process
GO:0009252 supplies the biological-process context for the D-glutamate and D-Ala-D-Ala precursors produced by this module.
PMID:30008699
A Broad Spectrum Racemase in Pseudomonas putida KT2440 Plays a Key Role in Amino Acid Catabolism.
The KT2440 Alr/BSR study establishes that measurable alanine racemase activity alone is insufficient to assign a physiological cytoplasmic D-alanine-supply role because Q88GJ9 is periplasmic and functions primarily in basic-amino-acid catabolism.
PMID:23995642
Amino acid racemization in Pseudomonas putida KT2440
The comparative racemase study establishes the unusual division between an alanine-specific DadX and a periplasmic broad-spectrum Alr in KT2440.
6Nodes
3Parts
1Variant Sets
2Variants
4Annotons
1Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:d_amino_acid_cell_wall_precursor_supply 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.

Function consistency and core coverage

5 gene-function check(s) reflected in core functions · 0 conflict(s) · 5 evidence or coverage gap(s) (10 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
murI_glutamate_racemase PSEPK MurI
UniProtKB:Q88PW2
Family Representative 		glutamate racemase activity
GO:0008881 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
murI_glutamate_racemase murI (Escherichia coli K-12)
UniProtKB:P22634
Family Representative 		glutamate racemase activity
GO:0008881 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
alr_biosynthetic_alanine_racemase Escherichia coli K-12 Alr
UniProtKB:P0A6B4
Family Representative 		alanine racemase activity
GO:0008784 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ddla_like_activity PSEPK DdlA
UniProtKB:Q88EV6
Family Representative 		D-alanine-D-alanine ligase activity
GO:0008716 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ddlb_like_activity PSEPK DdlB
UniProtKB:Q88N74
Family Representative 		D-alanine-D-alanine ligase activity
GO:0008716 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ddlb_like_activity PSEPK Ddl PP_5673
UniProtKB:A0A140FWM5
Family Representative 		D-alanine-D-alanine ligase activity
GO:0008716 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
murI_glutamate_racemase glutamate racemase subfamily
PANTHER:PTHR21198:SF2
Family 		glutamate racemase activity
GO:0008881 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR21198:SF2.
alr_biosynthetic_alanine_racemase biosynthetic alanine racemase family
PANTHER:PTHR30511:SF4
Family 		alanine racemase activity
GO:0008784 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR30511:SF4.
ddla_like_activity DdlA-like D-alanine-D-alanine ligases
PANTHER:PTHR23132:SF25
Family 		D-alanine-D-alanine ligase activity
GO:0008716 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR23132:SF25.
ddlb_like_activity DdlB-like D-alanine-D-alanine ligases
PANTHER:PTHR23132:SF23
Family 		D-alanine-D-alanine ligase activity
GO:0008716 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR23132:SF23.

Gene-review completeness (5/6 grounded genes reviewed)

5 complete review(s) · 3 with deep research · 1 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
ddl A0A140FWM5 ✓ ✓ ✗
ddlA Q88EV6 ✓ ✓ ✓
ddlB Q88N74 ✓ ✓ ✓
murI P22634 ✓ ✓ ✗
murI Q88PW2 ✓ ✓ ✓
Escherichia coli K-12 Alr P0A6B4 ✗ — —

Details

D-amino-acid supply for peptidoglycan precursor biosynthesisMetabolic Pathwayd_amino_acid_cell_wall_precursor_supply
peptidoglycan biosynthetic processGO:0009252

The module is species-neutral. Exact PSEPK proteins are representative members only where current evidence supports their chemistry. The two Ddl-family variants reflect resolved PANTHER subfamilies and possible redundancy, not different reactions. A0A140FWM5 is a second PSEPK representative of the DdlB-like branch, supported by HAMAP, Rhea, domain, signature, and catalytic-site evidence despite its unreviewed status. D-glutamate and D-Ala-D-Ala converge downstream in the Mur ligase pathway but are not represented as a false linear chain.

Connections

Alanine racemase supplies both D-alanine substrates used by Ddl.
Part 1: D-glutamate production
D-glutamate production by glutamate racemaseReactiond_glutamate_production

Annotons

glutamate racemase
murI_glutamate_racemase
Participant: Family: glutamate racemase subfamily
Family:
glutamate racemase subfamilyPANTHER:PTHR21198:SF2
Representative Members: PSEPK MurIUniProtKB:Q88PW2 murI (Escherichia coli K-12)UniProtKB:P22634

Function

glutamate racemase activityGO:0008881
Substrates: L-glutamate
Products: D-glutamate

Processes

peptidoglycan biosynthetic processGO:0009252

Produces the D-glutamate incorporated into the second position of the peptidoglycan stem peptide.

Part 2: D-alanine production
D-alanine production by a cytoplasmic alanine racemaseReactiond_alanine_production

Annotons

biosynthetic alanine racemase
alr_biosynthetic_alanine_racemase
Participant: Family: biosynthetic alanine racemase family
Family:
biosynthetic alanine racemase familyPANTHER:PTHR30511:SF4
Representative Members: Escherichia coli K-12 AlrUniProtKB:P0A6B4

Function

alanine racemase activityGO:0008784
Substrates: L-alanine
Products: D-alanine
Cofactors: pyridoxal 5'-phosphate

Processes

D-alanine biosynthetic processGO:0030632

Produces cytoplasmic D-alanine for D-Ala-D-Ala synthesis. A species-specific racemase is not assigned to this leaf solely from detectable in-vitro alanine racemase activity.

Part 3: D-Ala-D-Ala ligation
D-Ala-D-Ala ligationReactiond_ala_d_ala_ligation
Variant set: redundant D-alanine-D-alanine ligase family variants by Ddl orthology branch (One Or More)
DdlA-like D-alanine-D-alanine ligaseReactionddla_like_ligase

Annotons

DdlA-like D-alanine-D-alanine ligase
ddla_like_activity
Participant: Family: DdlA-like D-alanine-D-alanine ligases
Family:
DdlA-like D-alanine-D-alanine ligasesPANTHER:PTHR23132:SF25
Representative Members: PSEPK DdlAUniProtKB:Q88EV6

Function

D-alanine-D-alanine ligase activityGO:0008716
Substrates: D-alanine ATP
Products: D-alanyl-D-alanine ADP phosphate
Cofactors: magnesium or manganese ion

Processes

peptidoglycan biosynthetic processGO:0009252

Ligates two D-alanine molecules to form the dipeptide used by MurF.

DdlB-like D-alanine-D-alanine ligaseReactionddlb_like_ligase

Annotons

DdlB-like D-alanine-D-alanine ligase
ddlb_like_activity
Participant: Family: DdlB-like D-alanine-D-alanine ligases
Family:
DdlB-like D-alanine-D-alanine ligasesPANTHER:PTHR23132:SF23
Representative Members: PSEPK DdlBUniProtKB:Q88N74 PSEPK Ddl PP_5673UniProtKB:A0A140FWM5

Function

D-alanine-D-alanine ligase activityGO:0008716
Substrates: D-alanine ATP
Products: D-alanyl-D-alanine ADP phosphate
Cofactors: magnesium or manganese ion

Processes

peptidoglycan biosynthetic processGO:0009252

Ligates two D-alanine molecules to form the dipeptide used by MurF.