Pseudomonas-type anabolic peptidoglycan recycling

A reusable Gram-negative bacterial recycling route that imports soluble anhydromuropeptides, separates their GlcNAc, anhMurNAc, and stem-peptide components, and returns both MurNAc and the recovered peptide to peptidoglycan precursor synthesis. The sugar arm uses AnmK, MupP, AmgK, and MurU to regenerate UDP-MurNAc. This anabolic branch is characteristic of Pseudomonas and other bacteria that lack the MurQ catabolic diversion. Periplasmic generation of turnover fragments and downstream polymerization of peptidoglycan are outside the boundary.

MODULE:peptidoglycan_recyclingDRAFTCONCRETEMetabolic Pathwaymodules/peptidoglycan_recycling.yaml
peptidoglycan turnoverGO:0009254
GO:0009254
peptidoglycan turnover
Defines the biological-process boundary for recovery of cell-wall material.
PMID:23831760
A cell wall recycling shortcut that bypasses peptidoglycan de novo biosynthesis.
Direct P. putida work establishes AmgK and MurU as a salvage shortcut that channels MurNAc to UDP-MurNAc.
The anomeric sugar kinase AmgK and the MurNAc α-1-phosphate uridylyl transferase MurU
PMID:28351914
The N-Acetylmuramic Acid 6-Phosphate Phosphatase MupP Completes the Pseudomonas Peptidoglycan Recycling Pathway Leading to Intrinsic Fosfomycin Resistance.
Full-text target-species evidence establishes MupP and gives the complete P. putida pathway model from AmpG import through the anabolic sugar arm.
specifically converts MurNAc 6-phosphate to MurNAc
file:projects/P_PUTIDA/deep-research/PSEPK__peptidoglycan-recycling__ppu00520-deep-research-openscientist.md
OpenScientist PSEPK peptidoglycan-recycling synthesis
Species-aware retrieval used to distinguish the eight recycling members from broad KEGG nucleotide-sugar spillover and from MurA/MurB de novo synthesis.
RHEA:24952
AnmK reaction
Defines ring opening and phosphorylation of anhMurNAc to MurNAc-6-phosphate.
RHEA:53728
MupP reaction
Defines hydrolysis of MurNAc-6-phosphate to MurNAc and phosphate.
RHEA:53720
AmgK MurNAc reaction
Defines C1 phosphorylation of MurNAc to MurNAc-alpha-1-phosphate.
RHEA:53716
MurU reaction
Defines uridylyl transfer yielding UDP-MurNAc.
RHEA:29563
Mpl reaction
Defines ligation of the recovered stem tripeptide to UDP-MurNAc.

The module models an anabolic wall-to-wall recycling route. MurA and MurB are de novo UDP-MurNAc enzymes and are deliberately excluded. MurQ is not a required alternate part because it diverts MurNAc-6-phosphate to catabolism and is absent from the P. putida instance. The catabolic MurP/AnmK-MurQ-MurR route is modeled separately in MODULE:murnac_6p_catabolic_recycling. Lytic transglycosylases generate the imported substrate upstream but form a many-paralog turnover system rather than a single required leaf in this module. No generic cytoplasm or membrane term is asserted at module level; locations belong to individual activities.

9Nodes
8Parts
0Variant Sets
0Variants
8Annotons
9Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:peptidoglycan_recycling 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.

  • ampG_import_step → nagZ_glycan_processing_step [NOT_CHECKED]
    Imported muropeptides provide NagZ substrates.
  • ampG_import_step → ampD_peptide_release_step [NOT_CHECKED]
    Imported muropeptides provide AmpD substrates.
  • nagZ_glycan_processing_step → anmK_step [NOT_CHECKED]
    NagZ processing exposes the anhMurNAc-containing product.
  • ampD_peptide_release_step → anmK_step [NOT_CHECKED]
    AmpD releases peptide-free anhMurNAc for AnmK.
  • anmK_step → mupP_step [NOT_CHECKED]
    AnmK produces MurNAc-6-phosphate consumed by MupP.
  • mupP_step → amgK_step [NOT_CHECKED]
    MupP produces MurNAc consumed by AmgK.
  • amgK_step → murU_step [NOT_CHECKED]
    AmgK produces MurNAc-alpha-1-phosphate consumed by MurU.

Function consistency and core coverage

9 gene-function check(s) reflected in core functions · 0 conflict(s) · 14 evidence or coverage gap(s) (23 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
ampG_muropeptide_permease PSEPK AmpG
UniProtKB:Q88N61
Family Representative 		muropeptide transmembrane transporter activity
GO:0015647 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ampG_muropeptide_permease Escherichia coli AmpG
UniProtKB:P0AE16
Family Representative 		muropeptide transmembrane transporter activity
GO:0015647 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
nagZ_beta_hexosaminidase PSEPK NagZ
UniProtKB:Q88KZ4
Family Representative 		muropeptide beta-N-acetylglucosaminidase activity
GO:0016231 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
nagZ_beta_hexosaminidase Escherichia coli NagZ
UniProtKB:P75949
Family Representative 		muropeptide beta-N-acetylglucosaminidase activity
GO:0016231 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ampD_anhydromuramyl_amidase PSEPK AmpD
UniProtKB:Q88PQ9
Family Representative 		1,6-anhydro-N-acetylmuramyl-L-alanine amidase activity
GO:0008745 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ampD_anhydromuramyl_amidase Escherichia coli AmpD
UniProtKB:P13016
Family Representative 		1,6-anhydro-N-acetylmuramyl-L-alanine amidase activity
GO:0008745 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
anmK_activity PSEPK AnmK
UniProtKB:Q88QQ4
Family Representative 		1,6-anhydro-N-acetylmuramic acid kinase activity
GO:0016773 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
anmK_activity Escherichia coli AnmK
UniProtKB:P77570
Family Representative 		1,6-anhydro-N-acetylmuramic acid kinase activity
GO:0016773 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
mupP_activity PSEPK MupP
UniProtKB:Q88M11
Family Representative 		N-acetylmuramate 6-phosphate phosphatase activity
GO:0016791 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mupP_activity:required_function PSEPK MupP
UniProtKB:Q88M11
Family Representative 		N-acetylmuramate 6-phosphate phosphatase activity
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
amgK_activity PSEPK AmgK
UniProtKB:Q88QT3
Family Representative 		N-acetylmuramate anomeric kinase activity
GO:0019200 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
murU_activity PSEPK MurU
UniProtKB:Q88QT2
Family Representative 		N-acetylmuramate alpha-1-phosphate uridylyltransferase activity
GO:0070569 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mpl_activity PSEPK Mpl
UniProtKB:Q88QE7
Family Representative 		UDP-MurNAc-tripeptide ligase activity
GO:0106418 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mpl_activity Escherichia coli Mpl
UniProtKB:P37773
Family Representative 		UDP-MurNAc-tripeptide ligase activity
GO:0106418 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ampG_muropeptide_permease AmpG permease family
InterPro:IPR004752
Family 		muropeptide transmembrane transporter activity
GO:0015647 		Family Review Missing
No supported structured family review is available for InterPro:IPR004752.
nagZ_beta_hexosaminidase bacterial NagZ family
PANTHER:PTHR30480:SF13
Family 		muropeptide beta-N-acetylglucosaminidase activity
GO:0016231 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR30480:SF13.
ampD_anhydromuramyl_amidase AmpD recycling amidases
PANTHER:PTHR30417:SF4
Family 		1,6-anhydro-N-acetylmuramyl-L-alanine amidase activity
GO:0008745 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR30417:SF4.
anmK_activity AnmK family
PANTHER:PTHR30605:SF0
Family 		1,6-anhydro-N-acetylmuramic acid kinase activity
GO:0016773 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR30605:SF0.
mupP_activity MupP-like HAD_2 phosphatases
Pfam:PF13419
Family 		N-acetylmuramate 6-phosphate phosphatase activity
GO:0016791 		Family Review Missing
No supported structured family review is available for Pfam:PF13419.
mupP_activity:required_function MupP-like HAD_2 phosphatases
Pfam:PF13419
Family 		N-acetylmuramate 6-phosphate phosphatase activity
No function ID 		No Function Id
The family function has no GO identifier for comparison; prose is not matched.
amgK_activity AmgK anomeric sugar kinase subfamily
PANTHER:PTHR33540:SF1
Family 		N-acetylmuramate anomeric kinase activity
GO:0019200 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR33540:SF1.
murU_activity MurU family
InterPro:IPR054790
Family 		N-acetylmuramate alpha-1-phosphate uridylyltransferase activity
GO:0070569 		Family Review Missing
No supported structured family review is available for InterPro:IPR054790.
mpl_activity Mpl subfamily
PANTHER:PTHR43445:SF5
Family 		UDP-MurNAc-tripeptide ligase activity
GO:0106418 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR43445:SF5.

Gene-review completeness (9/13 grounded genes reviewed)

8 complete review(s) · 2 with deep research · 4 missing review · 7 reviewed but lacking deep research

Gene Review Complete Deep research
amgK Q88QT3 ✓ ✓ ✓
ampD Q88PQ9 ✓ ✓ ✗
ampG Q88N61 ✓ ✓ ✗
anmK Q88QQ4 ✓ ✓ ✗
mpl P37773 ✓ 14/15 ✗
mpl Q88QE7 ✓ ✓ ✗
mupP Q88M11 ✓ ✓ ✗
murU Q88QT2 ✓ ✓ ✓
nagZ Q88KZ4 ✓ ✓ ✗
Escherichia coli AmpG P0AE16 ✗ — —
Escherichia coli AmpD P13016 ✗ — —
Escherichia coli NagZ P75949 ✗ — —
Escherichia coli AnmK P77570 ✗ — —

Details

Pseudomonas-type anabolic peptidoglycan recyclingMetabolic Pathwaypeptidoglycan_recycling
peptidoglycan turnoverGO:0009254

Connections

anmK_step -> mupP_step Precedes
mupP_step -> amgK_step Precedes
amgK_step -> murU_step Precedes
ampD_peptide_release_step -> mpl_step Provides Input For
murU_step -> mpl_step Provides Input For
Part 1: anhydromuropeptide import
AmpG-mediated anhydromuropeptide importTransport StepampG_import_step

Annotons

AmpG muropeptide permease
ampG_muropeptide_permease
Participant: Family: AmpG permease family
Family:
AmpG permease familyInterPro:IPR004752
Representative Members: PSEPK AmpGUniProtKB:Q88N61 Escherichia coli AmpGUniProtKB:P0AE16

Function

muropeptide transmembrane transporter activityGO:0015647
Substrates: periplasmic GlcNAc-1,6-anhydro-MurNAc muropeptides
Products: cytoplasmic GlcNAc-1,6-anhydro-MurNAc muropeptides

Processes

peptidoglycan turnoverGO:0009254

Locations

plasma membraneGO:0005886

Moves soluble turnover fragments across the inner membrane.

Part 2: terminal GlcNAc removal
NagZ cleavage of muropeptide GlcNAcReactionnagZ_glycan_processing_step

Annotons

NagZ beta-N-acetylglucosaminidase
nagZ_beta_hexosaminidase
Participant: Family: bacterial NagZ family
Family:
bacterial NagZ familyPANTHER:PTHR30480:SF13
Representative Members: PSEPK NagZUniProtKB:Q88KZ4 Escherichia coli NagZUniProtKB:P75949

Function

muropeptide beta-N-acetylglucosaminidase activityGO:0016231
Substrates: GlcNAc-1,6-anhydro-MurNAc muropeptide water
Products: N-acetylglucosamine 1,6-anhydro-MurNAc peptide

Processes

peptidoglycan turnoverGO:0009254

Separates the glycan disaccharide into recyclable sugar components.

Part 3: stem-peptide release
AmpD cleavage of the anhMurNAc-stem bondReactionampD_peptide_release_step

Annotons

AmpD anhydromuramyl-L-alanine amidase
ampD_anhydromuramyl_amidase
Participant: Family: AmpD recycling amidases
Family:
AmpD recycling amidasesPANTHER:PTHR30417:SF4
Representative Members: PSEPK AmpDUniProtKB:Q88PQ9 Escherichia coli AmpDUniProtKB:P13016

Function

1,6-anhydro-N-acetylmuramyl-L-alanine amidase activityGO:0008745
Substrates: 1,6-anhydro-MurNAc-stem peptide water
Products: 1,6-anhydro-MurNAc peptidoglycan stem peptide

Processes

peptidoglycan turnoverGO:0009254

Splits the imported fragment into sugar and peptide salvage arms.

Part 4: anhMurNAc phosphorylation and ring opening
AnmK formation of MurNAc-6-phosphateReactionanmK_step

Annotons

Anhydro-N-acetylmuramic acid kinase
anmK_activity
Participant: Family: AnmK family
Family:
AnmK familyPANTHER:PTHR30605:SF0
Representative Members: PSEPK AnmKUniProtKB:Q88QQ4 Escherichia coli AnmKUniProtKB:P77570

Function

1,6-anhydro-N-acetylmuramic acid kinase activityGO:0016773
Substrates: 1,6-anhydro-N-acetylmuramic acid ATP water
Products: N-acetylmuramate 6-phosphate ADP proton

Processes

peptidoglycan turnoverGO:0009254

Commits recovered anhMurNAc to intracellular sugar salvage.

Part 5: MurNAc-6-phosphate dephosphorylation
MupP formation of MurNAcReactionmupP_step

Annotons

N-acetylmuramate 6-phosphate phosphatase
mupP_activity
Participant: Family: MupP-like HAD_2 phosphatases
Family:
MupP-like HAD_2 phosphatasesPfam:PF13419
Representative Members: PSEPK MupPUniProtKB:Q88M11
Required Function:
N-acetylmuramate 6-phosphate phosphatase activity

Function

N-acetylmuramate 6-phosphate phosphatase activityGO:0016791
Substrates: N-acetylmuramate 6-phosphate water
Products: N-acetylmuramate phosphate

Processes

peptidoglycan turnoverGO:0009254

Connects AnmK output to the AmgK-MurU anabolic shortcut.

Part 6: MurNAc anomeric phosphorylation
AmgK formation of MurNAc-alpha-1-phosphateReactionamgK_step

Annotons

N-acetylmuramate/N-acetylglucosamine kinase
amgK_activity
Participant: Family: AmgK anomeric sugar kinase subfamily
Family:
AmgK anomeric sugar kinase subfamilyPANTHER:PTHR33540:SF1
Representative Members: PSEPK AmgKUniProtKB:Q88QT3

Function

N-acetylmuramate anomeric kinase activityGO:0019200
Substrates: N-acetylmuramate ATP
Products: N-acetyl-alpha-D-muramate 1-phosphate ADP proton

Processes

peptidoglycan turnoverGO:0009254

Produces the anomeric phosphate accepted by MurU.

Part 7: UDP-MurNAc regeneration
MurU formation of UDP-MurNAcReactionmurU_step

Annotons

MurNAc-alpha-1-phosphate uridylyltransferase
murU_activity
Participant: Family: MurU family
Family:
MurU familyInterPro:IPR054790
Representative Members: PSEPK MurUUniProtKB:Q88QT2

Function

N-acetylmuramate alpha-1-phosphate uridylyltransferase activityGO:0070569
Substrates: N-acetyl-alpha-D-muramate 1-phosphate UDP proton
Products: UDP-N-acetylmuramate phosphate

Processes

peptidoglycan turnoverGO:0009254

Regenerates the activated sugar precursor UDP-MurNAc.

Part 8: recovered stem-peptide ligation
Mpl ligation of the recovered tripeptide to UDP-MurNAcReactionmpl_step

Annotons

Murein peptide ligase
mpl_activity
Participant: Family: Mpl subfamily
Family:
Mpl subfamilyPANTHER:PTHR43445:SF5
Representative Members: PSEPK MplUniProtKB:Q88QE7 Escherichia coli MplUniProtKB:P37773

Function

UDP-MurNAc-tripeptide ligase activityGO:0106418
Substrates: UDP-N-acetylmuramate L-Ala-gamma-D-Glu-meso-diaminopimelate ATP
Products: UDP-MurNAc-tripeptide ADP phosphate proton

Processes

peptidoglycan turnoverGO:0009254 peptidoglycan biosynthetic processGO:0009252

Rejoins the recovered peptide arm with the regenerated sugar precursor.