Low-molecular-mass PBP peptidoglycan hydrolysis

A reusable bacterial module for two distinct hydrolytic reactions performed by low-molecular-mass penicillin-binding proteins during peptidoglycan maturation. D,D-carboxypeptidases trim terminal D-alanine from uncrosslinked pentapeptide stems, whereas D,D-endopeptidases cleave D-Ala-mDAP 4-3 crosslinks between stems. Individual enzymes may catalyze one or both reactions; neither reaction represents protein proteolysis or crosslink formation.

MODULE:low_molecular_mass_pbp_peptidoglycan_hydrolysisDRAFTBiological Processmodules/low_molecular_mass_pbp_peptidoglycan_hydrolysis.yaml
peptidoglycan metabolic processGO:0000270
PMID:27716106
In vivo functional and molecular characterization of the Penicillin-Binding Protein 4 (DacB) of Pseudomonas aeruginosa.
Pseudomonas aeruginosa DacB/PBP4 catalyzes both reactions, with D,D-endopeptidase activity predominant.
LMM-PBP4 of Pseudomonas aeruginosa is a bifunctional enzyme presenting both D,D-carboxypeptidase and D,D-endopeptidase activities; the D,D-endopeptidase function is predominant.
PMID:8063800
Specific interaction of penicillin-binding proteins 3 and 7/8 with soluble lytic transglycosylase in Escherichia coli.
Escherichia coli PBP7/8 is an experimentally established D,D-endopeptidase.
PBP7/8, recently shown to be a DD-endopeptidase, bind to Slt70 in vitro.

The parts have equal order because stem trimming and crosslink hydrolysis are parallel remodeling reactions, not a compulsory linear sequence. DacB/PBP4 is intentionally represented in both parts because direct Pseudomonas experiments establish both activities. PbpG/PBP7 is represented only in the endopeptidase variant. GO:0009002 is not used as a proxy for crosslink hydrolysis because it names D,D-carboxypeptidase activity; GO:0061785 is used for the distinct peptidoglycan endopeptidase reaction.

5Nodes
2Parts
1Variant Sets
2Variants
3Annotons
0Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:low_molecular_mass_pbp_peptidoglycan_hydrolysis 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.

Gene-review completeness (2/4 grounded genes reviewed)

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

Gene Review Complete Deep research
dacB Q88L37 ✓ ✓ ✓
Escherichia coli PbpG/PBP7 P0AFI5 ✗ — —
pbpG Q88GD0 ✓ ✓ ✓
Pseudomonas aeruginosa DacB/PBP4 Q9HZG1 ✗ — —

Details

Context
bacteriaNCBITaxon:2
Low-molecular-mass PBP peptidoglycan hydrolysisBiological Processlow_molecular_mass_pbp_peptidoglycan_hydrolysis
peptidoglycan metabolic processGO:0000270
Context
bacteriaNCBITaxon:2
Part 1: pentapeptide stem trimming
Peptidoglycan pentapeptide stem trimmingReactionpentapeptide_stem_trimming

Annotons

DacB/PBP4 D,D-carboxypeptidase activity
dacb_dd_carboxypeptidase
Participant: Family: DacB/PBP4 peptidase S13 family
Family:
DacB/PBP4 peptidase S13 familyPANTHER:PTHR30023:SF0
Representative Members: PSEPK DacB/PBP4UniProtKB:Q88L37 Pseudomonas aeruginosa DacB/PBP4UniProtKB:Q9HZG1

Function

serine-type D,D-carboxypeptidase activityGO:0009002
Substrates: peptidoglycan pentapeptide stem water
Products: peptidoglycan tetrapeptide stem D-alanine

Processes

peptidoglycan metabolic processGO:0000270

Removes terminal D-alanine from an uncrosslinked pentapeptide stem.

Part 1: 4-3 peptidoglycan crosslink hydrolysis