id: P0AD65
gene_symbol: mrdA
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:83333
  label: Escherichia coli (strain K12)
description: >
  MrdA (also known as PBP2 or PbpA) is a class B penicillin-binding protein that functions
  as a
  monofunctional D,D-transpeptidase (EC 3.4.16.4) essential for lateral cell wall
  synthesis and
  rod shape determination in E. coli. It catalyzes the formation of 4-3 peptide crosslinks
  in
  peptidoglycan by transferring the terminal D-Ala from stem peptides to acceptor
  meso-diaminopimelate
  (mDAP) residues on neighboring glycan strands. MrdA works in partnership with RodA
  (a SEDS-family
  glycan polymerase) as the core elongasome synthase complex, with additional components
  including
  MreB, MreC, MreD, and RodZ. The protein is anchored in the inner membrane with its
  large catalytic
  domain exposed to the periplasm. MrdA is specifically inhibited by mecillinam (amdinocillin)
  and
  is also targeted by other beta-lactam antibiotics and diazabicyclooctane (DBO) inhibitors
  like
  avibactam. Loss of MrdA function causes cells to become spherical (cocci), demonstrating
  its
  essential role in maintaining rod morphology.
existing_annotations:
# ============== CELLULAR COMPONENT ANNOTATIONS ==============
# GO:0005886 plasma membrane - IBA
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >
        MrdA/PBP2 is an inner membrane protein with a single transmembrane helix (residues
        22-42)
        anchoring the periplasmic catalytic domain. UniProt confirms subcellular location
        as
        Cell inner membrane; Single-pass membrane protein.
      action: ACCEPT
      reason: >
        The plasma membrane (inner membrane in Gram-negative bacteria) localization
        is well-established
        through multiple experimental studies. The IBA annotation is phylogenetically
        consistent with
        experimental data.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "PBP2 is an inner-membrane bitopic protein with a large
            periplasmic catalytic domain"

# GO:0005886 plasma membrane - IEA
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >
        Automated annotation based on UniProtKB-SubCell and UniRule. Consistent with
        experimental evidence.
      action: ACCEPT
      reason: >
        The IEA annotation is correct and supported by multiple experimental studies
        confirming
        inner membrane localization. Keeping this as it reflects automated mapping
        that is accurate.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "PBP2 is an inner-membrane bitopic protein with a large
            periplasmic catalytic domain"

# GO:0005886 plasma membrane - IDA (PMID:37620344)
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: IDA
    original_reference_id: PMID:37620344
    review:
      summary: >
        Direct structural evidence from cryo-EM showing MrdA/PBP2 as a single-pass
        inner membrane protein
        in complex with RodA. The transmembrane helix anchors the protein to the plasma
        membrane.
      action: ACCEPT
      reason: >
        High-quality cryo-EM structure at 3.2 Angstroms resolution directly demonstrates
        the membrane
        topology and association of PBP2 with the inner membrane in complex with RodA.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Cell inner membrane"

# GO:0005886 plasma membrane - NAS (PMID:31915748)
        - reference_id: PMID:37620344
          supporting_text: Structural basis of peptidoglycan synthesis by E.
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: NAS
    original_reference_id: PMID:31915748
    review:
      summary: >
        Review article on RodZ function describes the elongasome complex at the plasma
        membrane.
      action: ACCEPT
      reason: >
        Non-traceable author statement in a review article, consistent with extensive
        experimental evidence.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Cell inner membrane"

# GO:0005886 plasma membrane - IDA (PMID:1103132)
        - reference_id: PMID:31915748
          supporting_text: 'eCollection 2019. RodZ: a key-player in cell elongation
            and cell division in Escherichia coli.'
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: IDA
    original_reference_id: PMID:1103132
    review:
      summary: >
        Classic 1975 Spratt paper identifying distinct penicillin-binding proteins
        in E. coli membranes,
        showing PBP2 is membrane-associated.
      action: ACCEPT
      reason: >
        Foundational experimental study demonstrating PBP2 is a membrane protein through
        biochemical
        fractionation and penicillin-binding assays on membrane preparations.
      supported_by:
        - reference_id: PMID:1103132
          supporting_text: "The varied effects of beta-lactam antibiotics on cell
            division, cell elongation, and cell shape in E. coli are shown to be due
            to the presence of three essential penicillin binding proteins"

# GO:0005886 plasma membrane - ISM (PMID:3533535)
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: ISM
    original_reference_id: PMID:3533535
    review:
      summary: >
        Sequence analysis identified transmembrane region in the deduced amino acid
        sequence of PBP2.
      action: ACCEPT
      reason: >
        Inferred from sequence model based on hydropathy analysis of the pbpA gene
        sequence,
        correctly predicting the transmembrane domain.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Nucleotide sequence of the pbpA gene and characteristics
            of the deduced amino acid sequence of penicillin-binding protein 2"

# GO:0016020 membrane - IEA
        - reference_id: PMID:3533535
          supporting_text: Nucleotide sequence of the pbpA gene and 
            characteristics of the deduced amino acid sequence of 
            penicillin-binding protein 2 of Escherichia coli K12.
  - term:
      id: GO:0016020
      label: membrane
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: >
        Generic membrane annotation from InterPro mapping. Too general given more
        specific
        plasma membrane annotations exist.
      action: MARK_AS_OVER_ANNOTATED
      reason: >
        This is a parent term of GO:0005886 (plasma membrane). Since multiple experimental
        and
        computational annotations already exist for the more specific term plasma
        membrane,
        this generic membrane annotation is redundant and less informative.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Cell inner membrane"

# GO:0030288 outer membrane-bounded periplasmic space - ISM
  - term:
      id: GO:0030288
      label: outer membrane-bounded periplasmic space
    evidence_type: ISM
    original_reference_id: PMID:3533535
    review:
      summary: >
        The large catalytic domain of MrdA (residues 43-633) is exposed to the periplasm
        where
        it catalyzes peptidoglycan crosslinking. This is where the enzymatic function
        occurs.
      action: ACCEPT
      reason: >
        Correct annotation - the periplasmic localization of the catalytic domain
        is essential
        for its function in peptidoglycan crosslinking. The topology is confirmed
        by sequence
        analysis and structural studies.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "PBP2 is an inner-membrane bitopic protein with a large
            periplasmic catalytic domain"

# ============== MOLECULAR FUNCTION ANNOTATIONS ==============
# GO:0008658 penicillin binding - IBA
        - reference_id: PMID:3533535
          supporting_text: Nucleotide sequence of the pbpA gene and 
            characteristics of the deduced amino acid sequence of 
            penicillin-binding protein 2 of Escherichia coli K12.
  - term:
      id: GO:0008658
      label: penicillin binding
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >
        MrdA/PBP2 is a penicillin-binding protein - this is the defining characteristic
        of PBPs.
        The active site serine (Ser330) forms a covalent acyl-enzyme intermediate
        with beta-lactam
        antibiotics.
      action: ACCEPT
      reason: >
        Core molecular function of this protein class. PBP2 binds penicillin and other
        beta-lactams
        at its active site serine, which is the basis for its inhibition by these
        antibiotics.
      supported_by:
        - reference_id: PMID:1103132
          supporting_text: "beta-Lactams that specifically result in the production
            of ovoid cells bind to penicillin binding protein 2"

# GO:0008658 penicillin binding - IEA
  - term:
      id: GO:0008658
      label: penicillin binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >
        Automated annotation based on InterPro domains and ARBA rules. Consistent
        with experimental data.
      action: ACCEPT
      reason: >
        Correct automated annotation supported by domain analysis and experimental
        evidence.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Penicillin-binding protein 2"

# GO:0008658 penicillin binding - IMP (PMID:37620344)
  - term:
      id: GO:0008658
      label: penicillin binding
    evidence_type: IMP
    original_reference_id: PMID:37620344
    review:
      summary: >
        Mutant phenotype analysis showing that S330A mutation abolishes binding to
        fluorescent
        penicillin mimic bocillin, demonstrating the active site serine is required
        for penicillin binding.
      action: ACCEPT
      reason: >
        Strong experimental evidence from mutagenesis demonstrating penicillin binding
        activity.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "S->A: No longer binds fluorescent penicillin mimic bocellin"

# GO:0008658 penicillin binding - IDA (PMID:1091862)
        - reference_id: PMID:37620344
          supporting_text: Structural basis of peptidoglycan synthesis by E.
  - term:
      id: GO:0008658
      label: penicillin binding
    evidence_type: IDA
    original_reference_id: PMID:1091862
    review:
      summary: >
        Direct biochemical demonstration of penicillin binding to PBP2.
      action: ACCEPT
      reason: >
        Classic experimental demonstration of penicillin binding activity.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Penicillin-binding protein 2"

# GO:0008658 penicillin binding - IDA (PMID:6243629)
        - reference_id: PMID:1091862
          supporting_text: Penicillin-binding proteins and cell shape in E.
  - term:
      id: GO:0008658
      label: penicillin binding
    evidence_type: IDA
    original_reference_id: PMID:6243629
    review:
      summary: >
        Identification of the mrdA gene cluster and demonstration that PBP2 binds
        mecillinam,
        a beta-lactam antibiotic.
      action: ACCEPT
      reason: >
        Experimental evidence showing specific beta-lactam binding to PBP2.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Inhibited by mecillinam and benzylpenicillin"

# GO:0008658 penicillin binding - IMP (PMID:1103132)
        - reference_id: PMID:6243629
          supporting_text: Cluster of mrdA and mrdB genes responsible for the 
            rod shape and mecillinam sensitivity of Escherichia coli.
  - term:
      id: GO:0008658
      label: penicillin binding
    evidence_type: IMP
    original_reference_id: PMID:1103132
    review:
      summary: >
        Mutant analysis showing correlation between beta-lactam binding to PBP2 and
        cell shape effects.
      action: ACCEPT
      reason: >
        Foundational study demonstrating penicillin binding through mutant phenotype
        analysis.
      supported_by:
        - reference_id: PMID:1103132
          supporting_text: "A mutant has been isolated that fails to bind beta-lactams
            to protein 2, and that grows as round cells"

# GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity - IEA
  - term:
      id: GO:0009002
      label: serine-type D-Ala-D-Ala carboxypeptidase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >
        MrdA/PBP2 is classified as EC 3.4.16.4 (serine-type D-Ala-D-Ala carboxypeptidase).
        This EC
        number encompasses the D,D-transpeptidase activity - the transpeptidation
        reaction involves
        cleavage of the D-Ala-D-Ala bond followed by transfer to an acceptor. This
        is the correct
        GO term for D,D-transpeptidase activity.
      action: ACCEPT
      reason: >
        This is the correct and most specific GO term for the D,D-transpeptidase activity
        of MrdA/PBP2.
        The enzyme catalyzes preferential cleavage at (Ac)2-L-Lys-D-Ala-D-Ala and
        also performs
        transpeptidation. GO does not have a separate D,D-transpeptidase activity
        term, so this
        EC-based term appropriately captures the molecular function.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "EC=3.4.16.4"

# GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity - IDA (PMID:30995398)
  - term:
      id: GO:0009002
      label: serine-type D-Ala-D-Ala carboxypeptidase activity
    evidence_type: IDA
    original_reference_id: PMID:30995398
    review:
      summary: >
        Structural and biochemical characterization of PBP2 catalytic activity and
        inhibition
        by DBO compounds at the active site.
      action: ACCEPT
      reason: >
        Direct demonstration of the enzymatic mechanism through structural and biochemical
        analysis.
      supported_by:
        - reference_id: PMID:30995398
          supporting_text: "describe the structure of the E. coli PBP2 in its Apo
            form"

# GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity - IDA (PMID:3009484)
  - term:
      id: GO:0009002
      label: serine-type D-Ala-D-Ala carboxypeptidase activity
    evidence_type: IDA
    original_reference_id: PMID:3009484
    review:
      summary: >
        Demonstration that PBP2 catalyzes peptidoglycan crosslinking (transpeptidation)
        in membrane
        preparations, sensitive to mecillinam inhibition.
      action: ACCEPT
      reason: >
        Key biochemical study demonstrating the transpeptidase activity of PBP2 in
        peptidoglycan
        synthesis.
      supported_by:
        - reference_id: PMID:3009484
          supporting_text: "The cross-linking reaction was strongly inhibited by the
            amidinopenicillin, mecillinam"

# GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity - IMP (PMID:1731901)
  - term:
      id: GO:0009002
      label: serine-type D-Ala-D-Ala carboxypeptidase activity
    evidence_type: IMP
    original_reference_id: PMID:1731901
    review:
      summary: >
        Active site residue characterization showing similarity to class A beta-lactamases
        in catalytic mechanism.
      action: ACCEPT
      reason: >
        Mutagenesis and mechanistic analysis demonstrating the serine-based catalytic
        mechanism.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "ACT_SITE        330"

# GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity - IDA (PMID:22606933)
        - reference_id: PMID:1731901
          supporting_text: 'Active-site residues of the transpeptidase domain of penicillin-binding
            protein 2 from Escherichia coli: similarity in catalytic mechanism to
            class A beta-lactamases.'
  - term:
      id: GO:0009002
      label: serine-type D-Ala-D-Ala carboxypeptidase activity
    evidence_type: IDA
    original_reference_id: PMID:22606933
    review:
      summary: >
        Biochemical demonstration that PBP2 has transpeptidase activity in the presence
        of
        active PBP1A, showing cooperativity of peptidoglycan synthases.
      action: ACCEPT
      reason: >
        Direct in vitro demonstration of transpeptidase activity in peptidoglycan
        synthesis assays.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "PBP2 is a D,D-transpeptidase that forms 4->3 peptide crosslinks"

# GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity - ISM (PMID:3533535)
        - reference_id: PMID:22606933
          supporting_text: Epub 2012 Jun 5. Cooperativity of peptidoglycan 
            synthases active in bacterial cell elongation.
  - term:
      id: GO:0009002
      label: serine-type D-Ala-D-Ala carboxypeptidase activity
    evidence_type: ISM
    original_reference_id: PMID:3533535
    review:
      summary: >
        Sequence analysis predicted transpeptidase domain with active site serine.
      action: ACCEPT
      reason: >
        Sequence-based prediction that has been validated by structural and biochemical
        studies.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Nucleotide sequence of the pbpA gene and characteristics
            of the deduced amino acid sequence of penicillin-binding protein 2"

# GO:0071972 peptidoglycan L,D-transpeptidase activity - IBA
        - reference_id: PMID:3533535
          supporting_text: Nucleotide sequence of the pbpA gene and 
            characteristics of the deduced amino acid sequence of 
            penicillin-binding protein 2 of Escherichia coli K12.
  - term:
      id: GO:0071972
      label: peptidoglycan L,D-transpeptidase activity
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >
        CRITICAL ERROR: MrdA/PBP2 is a D,D-transpeptidase, NOT an L,D-transpeptidase.
        L,D-transpeptidases (like YcbB/LdtD in E. coli) make 3-3 crosslinks between
        mDAP residues,
        while D,D-transpeptidases like PBP2 make 4-3 crosslinks (D-Ala position 4
        to mDAP position 3).
        UniProt explicitly names this protein Peptidoglycan D,D-transpeptidase MrdA
        (EC 3.4.16.4).
      action: REMOVE
      reason: >
        This annotation is biochemically incorrect. MrdA/PBP2 is definitively a D,D-transpeptidase
        that forms 4-3 peptide crosslinks, not an L,D-transpeptidase that forms 3-3
        crosslinks.
        The IBA may have been propagated from an incorrect ancestral annotation or
        misassignment.
        UniProt clearly states EC 3.4.16.4 (serine-type D-Ala-D-Ala carboxypeptidase)
        and names it
        Peptidoglycan D,D-transpeptidase MrdA. L,D-transpeptidases are a distinct
        enzyme family
        (e.g., YcbB/LdtD, YnhG/LdtE in E. coli) that do not use a serine nucleophile
        but instead
        use cysteine. The deep research confirms PBP2 forms 4-3 crosslinks, not 3-3
        crosslinks.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Peptidoglycan D,D-transpeptidase MrdA"
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "PBP2 is a D,D-transpeptidase that forms 4->3 peptide crosslinks"

# GO:0071972 peptidoglycan L,D-transpeptidase activity - IDA (PMID:6297485)
  - term:
      id: GO:0071972
      label: peptidoglycan L,D-transpeptidase activity
    evidence_type: IDA
    original_reference_id: PMID:6297485
    review:
      summary: >
        CRITICAL ERROR: The 1982 paper by Ishino et al. describes A mecillinam-sensitive
        peptidoglycan
        crosslinking reaction - this demonstrates D,D-transpeptidase activity (4-3
        crosslinks), NOT
        L,D-transpeptidase activity (3-3 crosslinks). The paper's title and content
        describe the
        crosslinking reaction of PBP2, which is a D,D-transpeptidase. The GO annotation
        appears to
        have been made in error, possibly due to confusion about crosslink nomenclature.
      action: REMOVE
      reason: >
        This annotation misinterprets the cited paper. PMID:6297485 demonstrates mecillinam-sensitive
        crosslinking by PBP2, which is D,D-transpeptidase activity, NOT L,D-transpeptidase
        activity.
        Mecillinam specifically inhibits PBP2, a D,D-transpeptidase. L,D-transpeptidases
        are resistant
        to beta-lactams. The annotation should be removed as it incorrectly characterizes
        the enzyme
        activity. GO does not currently have a D,D-transpeptidase activity term, so
        the correct
        annotation is GO:0009002 (serine-type D-Ala-D-Ala carboxypeptidase activity).
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Peptidoglycan D,D-transpeptidase MrdA"

# GO:0004180 carboxypeptidase activity - IEA
        - reference_id: PMID:6297485
          supporting_text: A mecillinam-sensitive peptidoglycan crosslinking 
            reaction in Escherichia coli.
  - term:
      id: GO:0004180
      label: carboxypeptidase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >
        Generic carboxypeptidase activity from UniProt keyword mapping. Too general
        when
        GO:0009002 (serine-type D-Ala-D-Ala carboxypeptidase activity) exists.
      action: MARK_AS_OVER_ANNOTATED
      reason: >
        This is a parent term of GO:0009002. The more specific term better describes
        the
        actual enzymatic activity and should be preferred. This generic term does
        not
        adequately convey the specialized D-Ala-D-Ala substrate specificity.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Carboxypeptidase"

# GO:0008233 peptidase activity - IEA
  - term:
      id: GO:0008233
      label: peptidase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >
        Very generic peptidase annotation from UniProt keyword mapping. Too general
        and potentially
        misleading as MrdA's primary function is transpeptidation (transfer), not
        simple hydrolysis.
      action: MARK_AS_OVER_ANNOTATED
      reason: >
        This high-level term is uninformative and potentially misleading. MrdA's primary
        biological
        function is transpeptidation (crosslinking peptidoglycan), not general peptidase
        activity.
        The more specific GO:0009002 should be used. Generic peptidase activity does
        not capture
        the essential transpeptidation function.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Protease"

# GO:0016787 hydrolase activity - IEA
  - term:
      id: GO:0016787
      label: hydrolase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >
        Very generic hydrolase annotation. MrdA has hydrolase activity in the mechanistic
        sense
        (the transpeptidation reaction proceeds through an acyl-enzyme intermediate),
        but this
        term is too generic to be informative.
      action: MARK_AS_OVER_ANNOTATED
      reason: >
        This is an extremely high-level parent term that provides no specific information
        about
        MrdA's function. The specific activity GO:0009002 should be preferred. While
        technically
        correct at a broad level, this annotation adds no value for understanding
        gene function.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Hydrolase"

# GO:0005515 protein binding - IPI (PMID:22606933) - first occurrence
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:22606933
    review:
      summary: >
        PBP2 interacts with PBP1A (P02918/mrcA). This interaction is functionally
        significant -
        PBP1A and PBP2 cooperate in peptidoglycan synthesis, and PBP2 stimulates PBP1A's
        glycosyltransferase activity.
      action: KEEP_AS_NON_CORE
      reason: >
        Per GO curation guidelines, protein binding is too vague. However, the interaction
        with PBP1A
        has functional significance in peptidoglycan synthesis cooperativity. Keeping
        as non-core
        to capture the documented interaction.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "P0AD65; P02918: mrcA; NbExp=5"

# GO:0005515 protein binding - IPI (PMID:37620344)
        - reference_id: PMID:22606933
          supporting_text: Epub 2012 Jun 5. Cooperativity of peptidoglycan 
            synthases active in bacterial cell elongation.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:37620344
    review:
      summary: >
        PBP2 interacts with RodA (P0ABG7) - this is the core elongasome synthase complex.
        The RodA-PBP2 interaction is essential for peptidoglycan synthesis during
        cell elongation.
      action: KEEP_AS_NON_CORE
      reason: >
        While protein binding is generally uninformative, the RodA-PBP2 interaction
        is
        functionally critical and documented with structural evidence (cryo-EM). This
        captures
        an important protein-protein interaction, though a more specific term would
        be preferable
        if available.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "It forms the RodA-PBP2 complex"

# GO:0005515 protein binding - IPI (PMID:33370261)
        - reference_id: PMID:37620344
          supporting_text: Structural basis of peptidoglycan synthesis by E.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:33370261
    review:
      summary: >
        PBP2 interacts with MreC (P16926). MreC and MreD balance the interaction between
        PBP2 and RodA, regulating elongasome activity.
      action: KEEP_AS_NON_CORE
      reason: >
        Captures important elongasome complex interaction, though protein binding
        is
        not optimally informative.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "MreC and MreD are periplasmic/inner-membrane factors that
            modulate RodA-PBP2 activity"

# GO:0005515 protein binding - IPI (PMID:10037771)
        - reference_id: PMID:33370261
          supporting_text: eCollection 2020 Dec.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:10037771
    review:
      summary: >
        PBP2 interacts with MipA (P0A935). This appears to be part of a larger murein
        synthesis complex.
      action: KEEP_AS_NON_CORE
      reason: >
        Documents protein-protein interaction relevant to cell wall synthesis machinery.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "PBP2 operates with its SEDS-family glycosyltransferase
            partner RodA as the core elongasome synthase"

# GO:0005515 protein binding - IPI (PMID:26396257)
        - reference_id: PMID:10037771
          supporting_text: Demonstration of molecular interactions between the 
            murein polymerase PBP1B, the lytic transglycosylase MltA, and the 
            scaffolding protein MipA of Escherichia coli.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:26396257
    review:
      summary: >
        PBP2 interacts with RodZ (P27434). RodZ links MreB to cell wall synthesis
        to
        mediate MreB rotation and morphogenesis.
      action: KEEP_AS_NON_CORE
      reason: >
        Documents interaction with RodZ, a key elongasome component.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "RodZ links MreB to the membrane and the complex"

# GO:0005515 protein binding - IPI (PMID:9158739)
        - reference_id: PMID:26396257
          supporting_text: RodZ links MreB to cell wall synthesis to mediate 
            MreB rotation and robust morphogenesis.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:9158739
    review:
      summary: >
        PBP2 interaction detected via affinity chromatography as part of multienzyme
        complexes in murein synthesis. Interacts with MltB (P0AGC3).
      action: KEEP_AS_NON_CORE
      reason: >
        Documents protein-protein interaction in murein synthesis complex.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "accessory components include MreB, MreC, MreD, and RodZ"

# ============== BIOLOGICAL PROCESS ANNOTATIONS ==============
# GO:0071555 cell wall organization - IBA
        - reference_id: PMID:9158739
          supporting_text: Affinity chromatography as a means to study 
            multienzyme complexes involved in murein synthesis.
  - term:
      id: GO:0071555
      label: cell wall organization
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >
        MrdA/PBP2 is essential for lateral cell wall synthesis and organization as
        part
        of the elongasome complex.
      action: ACCEPT
      reason: >
        Core biological process for this protein. PBP2 crosslinks peptidoglycan during
        cell wall elongation, directly organizing the cell wall structure.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "essential class B PBP and D,D-transpeptidase that catalyzes
            peptide crosslinking during lateral peptidoglycan (PG) synthesis"

# GO:0071555 cell wall organization - IEA
  - term:
      id: GO:0071555
      label: cell wall organization
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >
        Automated annotation from UniProt keyword mapping, consistent with experimental
        evidence.
      action: ACCEPT
      reason: >
        Correct automated annotation reflecting core function.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Cell wall biogenesis/degradation"

# GO:0071555 cell wall organization - IMP (PMID:18390656)
  - term:
      id: GO:0071555
      label: cell wall organization
    evidence_type: IMP
    original_reference_id: PMID:18390656
    review:
      summary: >
        Mutant phenotype analysis showing role in peptidoglycan organization during
        growth.
      action: ACCEPT
      reason: >
        Experimental evidence from mutant phenotype supporting role in cell wall organization.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Cell wall biogenesis/degradation"

# GO:0071555 cell wall organization - IMP (PMID:11418550)
        - reference_id: PMID:18390656
          supporting_text: 'Growth of Escherichia coli: significance of peptidoglycan
            degradation during elongation and septation.'
  - term:
      id: GO:0071555
      label: cell wall organization
    evidence_type: IMP
    original_reference_id: PMID:11418550
    review:
      summary: >
        Mutant analysis showing that impaired PBP2 activity leads to constitutive
        septal
        murein synthesis, demonstrating its role in organizing lateral vs septal growth.
      action: ACCEPT
      reason: >
        Experimental evidence showing how loss of PBP2 function disrupts normal cell
        wall organization patterns.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Cell wall biogenesis/degradation"

# GO:0009252 peptidoglycan biosynthetic process - IEA
        - reference_id: PMID:11418550
          supporting_text: Constitutive septal murein synthesis in Escherichia 
            coli with impaired activity of the morphogenetic proteins RodA and 
            penicillin-binding protein 2.
  - term:
      id: GO:0009252
      label: peptidoglycan biosynthetic process
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >
        Core biological process - MrdA/PBP2 catalyzes crosslinking during peptidoglycan
        biosynthesis.
      action: ACCEPT
      reason: >
        Correct automated annotation. PBP2 is essential for peptidoglycan biosynthesis,
        specifically the crosslinking step.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Cell wall biogenesis; peptidoglycan biosynthesis"

# GO:0009252 peptidoglycan biosynthetic process - IC (PMID:30995398)
  - term:
      id: GO:0009252
      label: peptidoglycan biosynthetic process
    evidence_type: IC
    original_reference_id: PMID:30995398
    review:
      summary: >
        Inferred from curator based on GO:0009002 (the molecular function implies
        involvement
        in this biological process).
      action: ACCEPT
      reason: >
        Valid IC annotation - the D-Ala-D-Ala carboxypeptidase/transpeptidase activity
        directly
        participates in peptidoglycan biosynthesis.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Cell wall biogenesis; peptidoglycan biosynthesis"

# GO:0009252 peptidoglycan biosynthetic process - IDA (PMID:3009484)
        - reference_id: PMID:30995398
          supporting_text: Epub 2019 Apr 26. Structural Basis for E.
  - term:
      id: GO:0009252
      label: peptidoglycan biosynthetic process
    evidence_type: IDA
    original_reference_id: PMID:3009484
    review:
      summary: >
        Direct biochemical demonstration of peptidoglycan synthesis by PBP2/RodA-containing
        membrane fractions.
      action: ACCEPT
      reason: >
        Key experimental demonstration of PBP2's role in peptidoglycan synthesis.
      supported_by:
        - reference_id: PMID:3009484
          supporting_text: "The cross-linked peptidoglycan was synthesized from UDP-N-acetylmuramylpentapeptide
            and UDP-N-acetylglucosamine"

# GO:0009252 peptidoglycan biosynthetic process - NAS (PMID:31915748)
  - term:
      id: GO:0009252
      label: peptidoglycan biosynthetic process
    evidence_type: NAS
    original_reference_id: PMID:31915748
    review:
      summary: >
        Review article describing PBP2's role in peptidoglycan biosynthesis as part
        of the
        elongasome.
      action: ACCEPT
      reason: >
        Non-traceable author statement consistent with experimental evidence.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "peptidoglycan biosynthesis"

# GO:0009252 peptidoglycan biosynthetic process - IDA (PMID:22606933)
        - reference_id: PMID:31915748
          supporting_text: 'eCollection 2019. RodZ: a key-player in cell elongation
            and cell division in Escherichia coli.'
  - term:
      id: GO:0009252
      label: peptidoglycan biosynthetic process
    evidence_type: IDA
    original_reference_id: PMID:22606933
    review:
      summary: >
        In vitro peptidoglycan synthesis assays demonstrating PBP2 transpeptidase
        activity
        and cooperation with PBP1A.
      action: ACCEPT
      reason: >
        Direct biochemical evidence of PBP2 function in peptidoglycan synthesis.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "peptidoglycan biosynthesis"

# GO:0009252 peptidoglycan biosynthetic process - IMP (PMID:18390656)
        - reference_id: PMID:22606933
          supporting_text: Epub 2012 Jun 5. Cooperativity of peptidoglycan 
            synthases active in bacterial cell elongation.
  - term:
      id: GO:0009252
      label: peptidoglycan biosynthetic process
    evidence_type: IMP
    original_reference_id: PMID:18390656
    review:
      summary: >
        Mutant phenotype analysis showing role in peptidoglycan synthesis during cell
        growth.
      action: ACCEPT
      reason: >
        Experimental evidence from mutant analysis.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "peptidoglycan biosynthesis"

# GO:0006508 proteolysis - IEA
        - reference_id: PMID:18390656
          supporting_text: 'Growth of Escherichia coli: significance of peptidoglycan
            degradation during elongation and septation.'
  - term:
      id: GO:0006508
      label: proteolysis
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >
        Generic proteolysis annotation from protease keyword. Misleading because MrdA's
        primary function is transpeptidation of peptidoglycan, not general proteolysis.
      action: REMOVE
      reason: >
        This annotation is misleading. While MrdA has carboxypeptidase activity mechanistically,
        its biological function is peptidoglycan crosslinking (transpeptidation),
        not
        proteolysis in the general sense. The term proteolysis suggests protein degradation
        which is not the function of this enzyme. GO:0009252 (peptidoglycan biosynthetic
        process)
        more accurately captures the biological role.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
          supporting_text: "PBP2 is a D,D-transpeptidase that forms 4->3 peptide crosslinks"

# GO:0008360 regulation of cell shape - IEA
  - term:
      id: GO:0008360
      label: regulation of cell shape
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >
        Core biological function - MrdA/PBP2 is essential for maintaining rod cell
        shape
        in E. coli.
      action: ACCEPT
      reason: >
        Essential and well-documented function. Loss of PBP2 causes cells to become
        spherical.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Responsible for the determination of the rod shape of
            the cell"

# GO:0008360 regulation of cell shape - IMP (PMID:3894330)
  - term:
      id: GO:0008360
      label: regulation of cell shape
    evidence_type: IMP
    original_reference_id: PMID:3894330
    review:
      summary: >
        Temperature-sensitive mrdA mutants show loss of rod shape at non-permissive
        temperature,
        growing as spherical cells (cocci).
      action: ACCEPT
      reason: >
        Classic genetic demonstration of PBP2's essential role in cell shape determination.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Temperature-sensitive mutants grow as normal rods at 30
            degrees Celsius but grow and divide as cocci during prolonged culturing
            at 42 degrees Celsius"

# GO:0008360 regulation of cell shape - NAS (PMID:31915748)
        - reference_id: PMID:3894330
          supporting_text: 'Cell shape and division in Escherichia coli: experiments
            with shape and division mutants.'
  - term:
      id: GO:0008360
      label: regulation of cell shape
    evidence_type: NAS
    original_reference_id: PMID:31915748
    review:
      summary: >
        Review describes PBP2 role in cell shape maintenance as part of the elongasome.
      action: ACCEPT
      reason: >
        Non-traceable author statement consistent with experimental evidence.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Cell shape"

# GO:0008360 regulation of cell shape - IMP (PMID:6243629)
        - reference_id: PMID:31915748
          supporting_text: 'eCollection 2019. RodZ: a key-player in cell elongation
            and cell division in Escherichia coli.'
  - term:
      id: GO:0008360
      label: regulation of cell shape
    evidence_type: IMP
    original_reference_id: PMID:6243629
    review:
      summary: >
        Identification of mrdA gene cluster and demonstration that it controls rod
        shape
        and mecillinam sensitivity.
      action: ACCEPT
      reason: >
        Foundational genetic study identifying mrdA as essential for rod shape.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Responsible for the determination of the rod shape of
            the cell"

# GO:0008360 regulation of cell shape - IMP (PMID:1103132)
        - reference_id: PMID:6243629
          supporting_text: Cluster of mrdA and mrdB genes responsible for the 
            rod shape and mecillinam sensitivity of Escherichia coli.
  - term:
      id: GO:0008360
      label: regulation of cell shape
    evidence_type: IMP
    original_reference_id: PMID:1103132
    review:
      summary: >
        Mutant analysis showing PBP2 is essential for rod shape - mutants that fail
        to
        bind beta-lactams to PBP2 grow as round cells.
      action: ACCEPT
      reason: >
        Classic experimental demonstration of PBP2 role in shape determination.
      supported_by:
        - reference_id: PMID:1103132
          supporting_text: "A mutant has been isolated that fails to bind beta-lactams
            to protein 2, and that grows as round cells"

# GO:0008360 regulation of cell shape - IMP (PMID:11418550)
  - term:
      id: GO:0008360
      label: regulation of cell shape
    evidence_type: IMP
    original_reference_id: PMID:11418550
    review:
      summary: >
        Impaired PBP2 activity leads to altered morphogenesis and constitutive septal
        synthesis.
      action: ACCEPT
      reason: >
        Mutant phenotype demonstrates role in cell shape regulation.
      supported_by:
        - reference_id: file:ECOLI/mrdA/mrdA-uniprot.txt
          supporting_text: "Cell shape"

# GO:0046677 response to antibiotic - IMP (PMID:1103132)
        - reference_id: PMID:11418550
          supporting_text: Constitutive septal murein synthesis in Escherichia 
            coli with impaired activity of the morphogenetic proteins RodA and 
            penicillin-binding protein 2.
  - term:
      id: GO:0046677
      label: response to antibiotic
    evidence_type: IMP
    original_reference_id: PMID:1103132
    review:
      summary: >
        PBP2 is the target of mecillinam and other beta-lactam antibiotics. The cellular
        response to mecillinam (spherical cell formation) is mediated through PBP2
        inhibition.
      action: ACCEPT
      reason: >
        Valid annotation - PBP2 is the direct target of mecillinam, and mutations
        in mrdA
        confer resistance. This captures the protein's role in antibiotic response.
      supported_by:
        - reference_id: PMID:1103132
          supporting_text: "beta-Lactams that specifically result in the production
            of ovoid cells bind to penicillin binding protein 2"

references:
  - id: GO_REF:0000002
    title: Gene Ontology annotation through association of InterPro records with
      GO terms
    findings: []
  - id: GO_REF:0000033
    title: Annotation inferences using phylogenetic trees
    findings: []
  - id: GO_REF:0000043
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword 
      mapping
    findings: []
  - id: GO_REF:0000120
    title: Combined Automated Annotation using Multiple IEA Methods
    findings: []
  - id: PMID:1091862
    title: Penicillin-binding proteins and cell shape in E. coli.
    findings: []
  - id: PMID:1103132
    title: Distinct penicillin binding proteins involved in the division, 
      elongation, and shape of Escherichia coli K12.
    findings:
      - statement: Foundational study identifying PBP2 as essential for rod 
          shape
        supporting_text: "The varied effects of beta-lactam antibiotics on cell division,
          cell elongation, and cell shape in E. coli are shown to be due to the presence
          of three essential penicillin binding proteins"
      - statement: Mutants failing to bind beta-lactams to PBP2 grow as round 
          cells
        supporting_text: "A mutant has been isolated that fails to bind beta-lactams
          to protein 2, and that grows as round cells"
      - statement: PBP2 is associated with cell elongation
        supporting_text: "beta-Lactams that specifically result in the production
          of ovoid cells bind to penicillin binding protein 2"
  - id: PMID:11418550
    title: Constitutive septal murein synthesis in Escherichia coli with 
      impaired activity of the morphogenetic proteins RodA and 
      penicillin-binding protein 2.
    findings: []
  - id: PMID:1731901
    title: "Active-site residues of the transpeptidase domain of penicillin-binding
      protein 2 from Escherichia coli: similarity in catalytic mechanism to class
      A beta-lactamases."
    findings: []
  - id: PMID:18390656
    title: "Growth of Escherichia coli: significance of peptidoglycan degradation
      during elongation and septation."
    findings: []
  - id: PMID:22606933
    title: Cooperativity of peptidoglycan synthases active in bacterial cell 
      elongation.
    findings: []
  - id: PMID:26396257
    title: RodZ links MreB to cell wall synthesis to mediate MreB rotation and 
      robust morphogenesis.
    findings: []
  - id: PMID:3009484
    title: Peptidoglycan synthetic activities in membranes of Escherichia coli 
      caused by overproduction of penicillin-binding protein 2 and rodA protein.
    findings:
      - statement: Demonstrated PBP2/RodA-dependent peptidoglycan synthesis
        supporting_text: "The cross-linked peptidoglycan was synthesized from UDP-N-acetylmuramylpentapeptide
          and UDP-N-acetylglucosamine"
      - statement: Cross-linking activity inhibited by mecillinam
        supporting_text: "The cross-linking reaction was strongly inhibited by the
          amidinopenicillin, mecillinam"
      - statement: Required both PBP2 and RodA for peptidoglycan formation
        supporting_text: "The formation of peptidoglycan required the presence of
          high levels of both PBP-2 and the RodA protein"
  - id: PMID:30995398
    title: Structural Basis for E. coli Penicillin Binding Protein (PBP) 2 
      Inhibition, a Platform for Drug Design.
    findings:
      - statement: Crystal structures of PBP2 apo and with inhibitors
        supporting_text: "describe the structure of the E. coli PBP2 in its Apo form"
  - id: PMID:3148617
    title: Identification of the penicillin-binding active site of 
      penicillin-binding protein 2 of Escherichia coli.
    findings: []
  - id: PMID:31915748
    title: "RodZ: a key-player in cell elongation and cell division in Escherichia
      coli."
    findings: []
  - id: PMID:33370261
    title: MreC and MreD balance the interaction between the elongasome proteins
      PBP2 and RodA.
    findings: []
  - id: PMID:3533535
    title: Nucleotide sequence of the pbpA gene and characteristics of the 
      deduced amino acid sequence of penicillin-binding protein 2 of Escherichia
      coli K12.
    findings: []
  - id: PMID:37620344
    title: Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 
      complex.
    findings: []
  - id: PMID:3894330
    title: "Cell shape and division in Escherichia coli: experiments with shape and
      division mutants."
    findings: []
  - id: PMID:6243629
    title: Cluster of mrdA and mrdB genes responsible for the rod shape and 
      mecillinam sensitivity of Escherichia coli.
    findings: []
  - id: PMID:6297485
    title: A mecillinam-sensitive peptidoglycan crosslinking reaction in 
      Escherichia coli.
    findings: []
  - id: PMID:9158739
    title: Affinity chromatography as a means to study multienzyme complexes 
      involved in murein synthesis.
    findings: []
  - id: PMID:10037771
    title: Demonstration of molecular interactions between the murein polymerase
      PBP1B, the lytic transglycosylase MltA, and the scaffolding protein MipA 
      of Escherichia coli.
    findings: []
  - id: file:ECOLI/mrdA/mrdA-deep-research-falcon.md
    title: Deep research on E. coli mrdA/PBP2
    findings:
      - statement: PBP2 is a D,D-transpeptidase
        supporting_text: "PBP2 is a D,D-transpeptidase that forms 4->3 peptide crosslinks"
      - statement: PBP2 is an inner membrane protein
        supporting_text: "PBP2 is an inner-membrane bitopic protein with a large periplasmic
          catalytic domain"
      - statement: PBP2 forms complex with RodA
        supporting_text: "It forms the RodA-PBP2 complex"

core_functions:
  - description: >
      MrdA/PBP2 is a D,D-transpeptidase (EC 3.4.16.4) that catalyzes the formation
      of 4-3
      peptide crosslinks in peptidoglycan. The reaction involves cleavage of the D-Ala-D-Ala
      bond and transfer of the acyl group to an acceptor mDAP residue. This is the
      core
      enzymatic function enabling peptidoglycan crosslinking during lateral cell wall
      synthesis.
    molecular_function:
      id: GO:0009002
      label: serine-type D-Ala-D-Ala carboxypeptidase activity
    directly_involved_in:
      - id: GO:0009252
        label: peptidoglycan biosynthetic process
      - id: GO:0008360
        label: regulation of cell shape
    locations:
      - id: GO:0005886
        label: plasma membrane
      - id: GO:0030288
        label: outer membrane-bounded periplasmic space
  - description: >
      MrdA/PBP2 is a penicillin-binding protein that covalently binds beta-lactam
      antibiotics
      at its active site serine (Ser330). This property is the basis for inhibition
      by
      mecillinam and other beta-lactams, and defines it as a member of the PBP family.
    molecular_function:
      id: GO:0008658
      label: penicillin binding
    directly_involved_in:
      - id: GO:0046677
        label: response to antibiotic
    locations:
      - id: GO:0005886
        label: plasma membrane

proposed_new_terms:
  - proposed_name: peptidoglycan D,D-transpeptidase activity
    proposed_definition: >
      Catalysis of the formation of 4-3 peptide crosslinks in peptidoglycan by transferring
      the penultimate D-alanine residue from position 4 of one stem peptide to the
      meso-diaminopimelate (mDAP) at position 3 of an acceptor stem peptide on a neighboring
      glycan strand. This is distinct from L,D-transpeptidase activity which forms
      3-3 crosslinks.
    justification: >
      GO currently has GO:0071972 (peptidoglycan L,D-transpeptidase activity) but
      no corresponding
      term for D,D-transpeptidase activity. D,D-transpeptidases (class B PBPs like
      MrdA/PBP2) and
      L,D-transpeptidases (like YcbB/LdtD) catalyze fundamentally different crosslinking
      reactions
      and have different substrate specificities, inhibitor sensitivities, and active
      site chemistry.
      A specific term would improve annotation accuracy. Currently GO:0009002 is used
      as a proxy
      but it emphasizes the carboxypeptidase aspect rather than the transpeptidation.
    proposed_parent:
      id: GO:0016755
      label: aminoacyltransferase activity

suggested_questions:
  - question: >
      Why was GO:0071972 (L,D-transpeptidase activity) annotated to MrdA/PBP2 when
      it is
      clearly a D,D-transpeptidase? Both IBA and IDA annotations exist for this term.
      The IDA cites
      PMID:6297485 which actually describes D,D-transpeptidase activity (mecillinam-sensitive
      crosslinking).
      This appears to be a significant annotation error that should be corrected.
  - question: >
      Should GO add a specific peptidoglycan D,D-transpeptidase activity term? D,D-transpeptidases
      and L,D-transpeptidases are mechanistically distinct enzymes with different
      active sites
      (serine vs cysteine), different crosslink products (4-3 vs 3-3), and different
      inhibitor
      sensitivities (beta-lactam sensitive vs resistant).

suggested_experiments: []