penicillin binding proteins

Name-to-sequence resolution

Record the organism, locus, accession, allele and sequence version behind each PBP alias.

1. Which species, strain, gene locus and protein sequence does this PBP designation identify? definition
2. Which curated record or primary experiment establishes the mapping between this alias and that sequence? provenance

PBP membership evidence

Assess domain architecture, catalytic-site features and functional evidence together, recording the classification scheme used.

1. Which sequence, structural or biochemical observations support PBP-family membership and subclass assignment? definition
2. What distinguishes this candidate from a beta-lactamase, L,D-transpeptidase or non-PBP glycan polymerase? boundary

Demonstrated catalytic function

Distinguish measured transpeptidation, carboxypeptidation, endopeptidation and glycan polymerization from inferred annotations.

1. Which bonds are formed or cleaved, and which measured products establish that reaction? measurement
2. Does the evidence attribute the reaction to this PBP rather than a copurified enzyme or complex partner? boundary

Native substrate relevance

Record substrate structure, reaction conditions and the limits of synthetic substrate surrogates.

1. Which stem peptide, cross-bridge, glycan context or lipid-linked substrate was tested, and how does it compare with the organism's peptidoglycan? boundary
2. What activity or kinetic parameters were measured at the stated pH, temperature, substrate concentration and membrane conditions? measurement

Productive complex membership

Distinguish association from functional dependence. Reconstituted FtsW polymerase activity required its cognate class B PBP in the reported experiments. [Primary study](https://www.nature.com/articles/s41564-018-0345-x)

1. Where is the PBP's catalytic domain located, and what evidence places the protein at septal, lateral or other cell-wall sites? measurement
2. Which partners are required for recruitment, activation or productive synthesis, and which merely associate under the tested conditions? boundary

Conditional function and redundancy

Record perturbation and rescue evidence without assuming every PBP is essential or functionally unique.

1. Under which strain and growth conditions does loss or inhibition alter viability, morphology or muropeptide composition? measurement
2. What complementation or compensating-PBP evidence supports the proposed physiological role? provenance

Compound-specific acylation

Record the compound, active-site modification, kinetic interpretation and any demonstrated regulatory effects. PBP2a studies establish a specific case of ceftaroline-associated allosteric opening; this is not a family-wide assumption. [Primary study](https://pubmed.ncbi.nlm.nih.gov/24085846/)

1. Which beta-lactam engages this PBP, with what exposure duration, occupancy and residual catalytic activity? measurement
2. Does the reported value describe acylation kinetics, equilibrium binding or a time-dependent competition assay? definition

Target change to cellular phenotype

Require evidence connecting the defined PBP change to the observed phenotype while retaining other resistance mechanisms as separate explanations.

1. What matched genetic and biochemical evidence connects this PBP variant or expression change to altered drug susceptibility? provenance
2. Which effects of beta-lactamase activity, permeability, efflux or other cell-wall changes remain unresolved? boundary
3. What resistance inference is justified by these data, and which inference requires additional organism-level testing? action

Preparation fitness

Record construct boundaries, tags, sequence changes, purity, aggregation and evidence for an active fraction.

1. Which native domains, membrane anchors or partner-binding regions are absent or modified in this preparation? boundary
2. What measurements establish protein identity, purity and catalytic competence? measurement
3. Is this preparation suitable for the proposed catalytic, binding or complex-assembly comparison? action

Orthogonal assay support

Separate band assignment, probe accessibility, product formation and whole-cell effects, preserving negative-result detection limits.

1. How was a fluorescent or radiolabeled band assigned to this PBP, and could comigration or probe accessibility explain the signal? provenance
2. Which independent product, occupancy or genetic measurement corroborates the interpretation, and what could remain undetected? measurement

Check these first

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these check these first hold for the sense of penicillin binding proteins this model covers, and on what evidence? provenance

Kinds and varieties

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these kinds and varieties hold for the sense of penicillin binding proteins this model covers, and on what evidence? provenance

Identifiers and schemes

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these identifiers and schemes hold for the sense of penicillin binding proteins this model covers, and on what evidence? provenance

Real-world use

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these real-world use hold for the sense of penicillin binding proteins this model covers, and on what evidence? provenance

Typical measurements

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these typical measurements hold for the sense of penicillin binding proteins this model covers, and on what evidence? provenance

Failure modes and hazards

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these failure modes and hazards hold for the sense of penicillin binding proteins this model covers, and on what evidence? provenance

Neighbouring kinds and how to tell them apart

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these neighbouring kinds and how to tell them apart hold for the sense of penicillin binding proteins this model covers, and on what evidence? provenance