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.
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.
Parent term: aminoacyltransferase activity
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | 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. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-deep-research-falcon.md PBP2 is an inner-membrane bitopic protein with a large periplasmic catalytic domain |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation based on UniProtKB-SubCell and UniRule. Consistent with experimental evidence. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-deep-research-falcon.md PBP2 is an inner-membrane bitopic protein with a large periplasmic catalytic domain |
| GO:0005886 plasma membrane | IDA PMID:37620344 Structural basis of peptidoglycan synthesis by E. coli RodA-... | ACCEPT | 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. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Cell inner membrane PMID:37620344 Structural basis of peptidoglycan synthesis by E. |
| GO:0005886 plasma membrane | NAS PMID:31915748 RodZ: a key-player in cell elongation and cell division in E... | ACCEPT | Summary: Review article on RodZ function describes the elongasome complex at the plasma membrane. Reason: Non-traceable author statement in a review article, consistent with extensive experimental evidence. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Cell inner membrane PMID:31915748 eCollection 2019. RodZ: a key-player in cell elongation and cell division in Escherichia coli. |
| GO:0005886 plasma membrane | IDA PMID:1103132 Distinct penicillin binding proteins involved in the divisio... | ACCEPT | Summary: Classic 1975 Spratt paper identifying distinct penicillin-binding proteins in E. coli membranes, showing PBP2 is membrane-associated. Reason: Foundational experimental study demonstrating PBP2 is a membrane protein through biochemical fractionation and penicillin-binding assays on membrane preparations. Supporting Evidence: PMID:1103132 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 Nucleotide sequence of the pbpA gene and characteristics of ... | ACCEPT | Summary: Sequence analysis identified transmembrane region in the deduced amino acid sequence of PBP2. Reason: Inferred from sequence model based on hydropathy analysis of the pbpA gene sequence, correctly predicting the transmembrane domain. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Nucleotide sequence of the pbpA gene and characteristics of the deduced amino acid sequence of penicillin-binding protein 2 PMID:3533535 Nucleotide sequence of the pbpA gene and characteristics of the deduced amino acid sequence of penicillin-binding protein 2 of Escherichia coli K12. |
| GO:0016020 membrane | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Generic membrane annotation from InterPro mapping. Too general given more specific plasma membrane annotations exist. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Cell inner membrane |
| GO:0030288 outer membrane-bounded periplasmic space | ISM PMID:3533535 Nucleotide sequence of the pbpA gene and characteristics of ... | ACCEPT | 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. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-deep-research-falcon.md PBP2 is an inner-membrane bitopic protein with a large periplasmic catalytic domain PMID:3533535 Nucleotide sequence of the pbpA gene and characteristics of the deduced amino acid sequence of penicillin-binding protein 2 of Escherichia coli K12. |
| GO:0008658 penicillin binding | IBA GO_REF:0000033 | ACCEPT | 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. 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. Supporting Evidence: PMID:1103132 beta-Lactams that specifically result in the production of ovoid cells bind to penicillin binding protein 2 |
| GO:0008658 penicillin binding | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation based on InterPro domains and ARBA rules. Consistent with experimental data. Reason: Correct automated annotation supported by domain analysis and experimental evidence. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Penicillin-binding protein 2 |
| GO:0008658 penicillin binding | IMP PMID:37620344 Structural basis of peptidoglycan synthesis by E. coli RodA-... | ACCEPT | 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. Reason: Strong experimental evidence from mutagenesis demonstrating penicillin binding activity. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt S->A: No longer binds fluorescent penicillin mimic bocellin PMID:37620344 Structural basis of peptidoglycan synthesis by E. |
| GO:0008658 penicillin binding | IDA PMID:1091862 Penicillin-binding proteins and cell shape in E. coli. | ACCEPT | Summary: Direct biochemical demonstration of penicillin binding to PBP2. Reason: Classic experimental demonstration of penicillin binding activity. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Penicillin-binding protein 2 PMID:1091862 Penicillin-binding proteins and cell shape in E. |
| GO:0008658 penicillin binding | IDA PMID:6243629 Cluster of mrdA and mrdB genes responsible for the rod shape... | ACCEPT | Summary: Identification of the mrdA gene cluster and demonstration that PBP2 binds mecillinam, a beta-lactam antibiotic. Reason: Experimental evidence showing specific beta-lactam binding to PBP2. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Inhibited by mecillinam and benzylpenicillin PMID:6243629 Cluster of mrdA and mrdB genes responsible for the rod shape and mecillinam sensitivity of Escherichia coli. |
| GO:0008658 penicillin binding | IMP PMID:1103132 Distinct penicillin binding proteins involved in the divisio... | ACCEPT | Summary: Mutant analysis showing correlation between beta-lactam binding to PBP2 and cell shape effects. Reason: Foundational study demonstrating penicillin binding through mutant phenotype analysis. Supporting Evidence: PMID:1103132 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 GO_REF:0000120 | ACCEPT | 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. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt EC=3.4.16.4 |
| GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity | IDA PMID:30995398 Structural Basis for E. coli Penicillin Binding Protein (PBP... | ACCEPT | Summary: Structural and biochemical characterization of PBP2 catalytic activity and inhibition by DBO compounds at the active site. Reason: Direct demonstration of the enzymatic mechanism through structural and biochemical analysis. Supporting Evidence: PMID:30995398 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 Peptidoglycan synthetic activities in membranes of Escherich... | ACCEPT | Summary: Demonstration that PBP2 catalyzes peptidoglycan crosslinking (transpeptidation) in membrane preparations, sensitive to mecillinam inhibition. Reason: Key biochemical study demonstrating the transpeptidase activity of PBP2 in peptidoglycan synthesis. Supporting Evidence: PMID:3009484 The cross-linking reaction was strongly inhibited by the amidinopenicillin, mecillinam |
| GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity | IMP PMID:1731901 Active-site residues of the transpeptidase domain of penicil... | ACCEPT | Summary: Active site residue characterization showing similarity to class A beta-lactamases in catalytic mechanism. Reason: Mutagenesis and mechanistic analysis demonstrating the serine-based catalytic mechanism. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt ACT_SITE 330 PMID:1731901 Active-site residues of the transpeptidase domain of penicillin-binding protein 2 from Escherichia coli: similarity in catalytic mechanism to class A beta-lactamases. |
| GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity | IDA PMID:22606933 Cooperativity of peptidoglycan synthases active in bacterial... | ACCEPT | Summary: Biochemical demonstration that PBP2 has transpeptidase activity in the presence of active PBP1A, showing cooperativity of peptidoglycan synthases. Reason: Direct in vitro demonstration of transpeptidase activity in peptidoglycan synthesis assays. Supporting Evidence: file:ECOLI/mrdA/mrdA-deep-research-falcon.md PBP2 is a D,D-transpeptidase that forms 4->3 peptide crosslinks PMID:22606933 Epub 2012 Jun 5. Cooperativity of peptidoglycan synthases active in bacterial cell elongation. |
| GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity | ISM PMID:3533535 Nucleotide sequence of the pbpA gene and characteristics of ... | ACCEPT | Summary: Sequence analysis predicted transpeptidase domain with active site serine. Reason: Sequence-based prediction that has been validated by structural and biochemical studies. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Nucleotide sequence of the pbpA gene and characteristics of the deduced amino acid sequence of penicillin-binding protein 2 PMID:3533535 Nucleotide sequence of the pbpA gene and characteristics of the deduced amino acid sequence of penicillin-binding protein 2 of Escherichia coli K12. |
| GO:0071972 peptidoglycan L,D-transpeptidase activity | IBA GO_REF:0000033 | REMOVE | 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). 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Peptidoglycan D,D-transpeptidase MrdA file:ECOLI/mrdA/mrdA-deep-research-falcon.md PBP2 is a D,D-transpeptidase that forms 4->3 peptide crosslinks |
| GO:0071972 peptidoglycan L,D-transpeptidase activity | IDA PMID:6297485 A mecillinam-sensitive peptidoglycan crosslinking reaction i... | REMOVE | 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. 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). Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Peptidoglycan D,D-transpeptidase MrdA PMID:6297485 A mecillinam-sensitive peptidoglycan crosslinking reaction in Escherichia coli. |
| GO:0004180 carboxypeptidase activity | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: Generic carboxypeptidase activity from UniProt keyword mapping. Too general when GO:0009002 (serine-type D-Ala-D-Ala carboxypeptidase activity) exists. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Carboxypeptidase |
| GO:0008233 peptidase activity | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | 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. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Protease |
| GO:0016787 hydrolase activity | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | 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. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Hydrolase |
| GO:0005515 protein binding | IPI PMID:22606933 Cooperativity of peptidoglycan synthases active in bacterial... | KEEP AS NON CORE | 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. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt P0AD65; P02918: mrcA; NbExp=5 PMID:22606933 Epub 2012 Jun 5. Cooperativity of peptidoglycan synthases active in bacterial cell elongation. |
| GO:0005515 protein binding | IPI PMID:37620344 Structural basis of peptidoglycan synthesis by E. coli RodA-... | KEEP AS NON CORE | 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. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-deep-research-falcon.md It forms the RodA-PBP2 complex PMID:37620344 Structural basis of peptidoglycan synthesis by E. |
| GO:0005515 protein binding | IPI PMID:33370261 MreC and MreD balance the interaction between the elongasome... | KEEP AS NON CORE | Summary: PBP2 interacts with MreC (P16926). MreC and MreD balance the interaction between PBP2 and RodA, regulating elongasome activity. Reason: Captures important elongasome complex interaction, though protein binding is not optimally informative. Supporting Evidence: file:ECOLI/mrdA/mrdA-deep-research-falcon.md MreC and MreD are periplasmic/inner-membrane factors that modulate RodA-PBP2 activity PMID:33370261 eCollection 2020 Dec. |
| GO:0005515 protein binding | IPI PMID:10037771 Demonstration of molecular interactions between the murein p... | KEEP AS NON CORE | Summary: PBP2 interacts with MipA (P0A935). This appears to be part of a larger murein synthesis complex. Reason: Documents protein-protein interaction relevant to cell wall synthesis machinery. Supporting Evidence: file:ECOLI/mrdA/mrdA-deep-research-falcon.md PBP2 operates with its SEDS-family glycosyltransferase partner RodA as the core elongasome synthase PMID:10037771 Demonstration of molecular interactions between the murein polymerase PBP1B, the lytic transglycosylase MltA, and the scaffolding protein MipA of Escherichia coli. |
| GO:0005515 protein binding | IPI PMID:26396257 RodZ links MreB to cell wall synthesis to mediate MreB rotat... | KEEP AS NON CORE | Summary: PBP2 interacts with RodZ (P27434). RodZ links MreB to cell wall synthesis to mediate MreB rotation and morphogenesis. Reason: Documents interaction with RodZ, a key elongasome component. Supporting Evidence: file:ECOLI/mrdA/mrdA-deep-research-falcon.md RodZ links MreB to the membrane and the complex PMID:26396257 RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis. |
| GO:0005515 protein binding | IPI PMID:9158739 Affinity chromatography as a means to study multienzyme comp... | KEEP AS NON CORE | Summary: PBP2 interaction detected via affinity chromatography as part of multienzyme complexes in murein synthesis. Interacts with MltB (P0AGC3). Reason: Documents protein-protein interaction in murein synthesis complex. Supporting Evidence: file:ECOLI/mrdA/mrdA-deep-research-falcon.md accessory components include MreB, MreC, MreD, and RodZ PMID:9158739 Affinity chromatography as a means to study multienzyme complexes involved in murein synthesis. |
| GO:0071555 cell wall organization | IBA GO_REF:0000033 | ACCEPT | Summary: MrdA/PBP2 is essential for lateral cell wall synthesis and organization as part of the elongasome complex. Reason: Core biological process for this protein. PBP2 crosslinks peptidoglycan during cell wall elongation, directly organizing the cell wall structure. Supporting Evidence: file:ECOLI/mrdA/mrdA-deep-research-falcon.md essential class B PBP and D,D-transpeptidase that catalyzes peptide crosslinking during lateral peptidoglycan (PG) synthesis |
| GO:0071555 cell wall organization | IEA GO_REF:0000043 | ACCEPT | Summary: Automated annotation from UniProt keyword mapping, consistent with experimental evidence. Reason: Correct automated annotation reflecting core function. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Cell wall biogenesis/degradation |
| GO:0071555 cell wall organization | IMP PMID:18390656 Growth of Escherichia coli: significance of peptidoglycan de... | ACCEPT | Summary: Mutant phenotype analysis showing role in peptidoglycan organization during growth. Reason: Experimental evidence from mutant phenotype supporting role in cell wall organization. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Cell wall biogenesis/degradation PMID:18390656 Growth of Escherichia coli: significance of peptidoglycan degradation during elongation and septation. |
| GO:0071555 cell wall organization | IMP PMID:11418550 Constitutive septal murein synthesis in Escherichia coli wit... | ACCEPT | Summary: Mutant analysis showing that impaired PBP2 activity leads to constitutive septal murein synthesis, demonstrating its role in organizing lateral vs septal growth. Reason: Experimental evidence showing how loss of PBP2 function disrupts normal cell wall organization patterns. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Cell wall biogenesis/degradation PMID:11418550 Constitutive septal murein synthesis in Escherichia coli with impaired activity of the morphogenetic proteins RodA and penicillin-binding protein 2. |
| GO:0009252 peptidoglycan biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Core biological process - MrdA/PBP2 catalyzes crosslinking during peptidoglycan biosynthesis. Reason: Correct automated annotation. PBP2 is essential for peptidoglycan biosynthesis, specifically the crosslinking step. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Cell wall biogenesis; peptidoglycan biosynthesis |
| GO:0009252 peptidoglycan biosynthetic process | IC PMID:30995398 Structural Basis for E. coli Penicillin Binding Protein (PBP... | ACCEPT | Summary: Inferred from curator based on GO:0009002 (the molecular function implies involvement in this biological process). Reason: Valid IC annotation - the D-Ala-D-Ala carboxypeptidase/transpeptidase activity directly participates in peptidoglycan biosynthesis. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Cell wall biogenesis; peptidoglycan biosynthesis PMID:30995398 Epub 2019 Apr 26. Structural Basis for E. |
| GO:0009252 peptidoglycan biosynthetic process | IDA PMID:3009484 Peptidoglycan synthetic activities in membranes of Escherich... | ACCEPT | Summary: Direct biochemical demonstration of peptidoglycan synthesis by PBP2/RodA-containing membrane fractions. Reason: Key experimental demonstration of PBP2's role in peptidoglycan synthesis. Supporting Evidence: PMID:3009484 The cross-linked peptidoglycan was synthesized from UDP-N-acetylmuramylpentapeptide and UDP-N-acetylglucosamine |
| GO:0009252 peptidoglycan biosynthetic process | NAS PMID:31915748 RodZ: a key-player in cell elongation and cell division in E... | ACCEPT | Summary: Review article describing PBP2's role in peptidoglycan biosynthesis as part of the elongasome. Reason: Non-traceable author statement consistent with experimental evidence. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt peptidoglycan biosynthesis PMID:31915748 eCollection 2019. RodZ: a key-player in cell elongation and cell division in Escherichia coli. |
| GO:0009252 peptidoglycan biosynthetic process | IDA PMID:22606933 Cooperativity of peptidoglycan synthases active in bacterial... | ACCEPT | Summary: In vitro peptidoglycan synthesis assays demonstrating PBP2 transpeptidase activity and cooperation with PBP1A. Reason: Direct biochemical evidence of PBP2 function in peptidoglycan synthesis. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt peptidoglycan biosynthesis PMID:22606933 Epub 2012 Jun 5. Cooperativity of peptidoglycan synthases active in bacterial cell elongation. |
| GO:0009252 peptidoglycan biosynthetic process | IMP PMID:18390656 Growth of Escherichia coli: significance of peptidoglycan de... | ACCEPT | Summary: Mutant phenotype analysis showing role in peptidoglycan synthesis during cell growth. Reason: Experimental evidence from mutant analysis. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt peptidoglycan biosynthesis PMID:18390656 Growth of Escherichia coli: significance of peptidoglycan degradation during elongation and septation. |
| GO:0006508 proteolysis | IEA GO_REF:0000043 | REMOVE | Summary: Generic proteolysis annotation from protease keyword. Misleading because MrdA's primary function is transpeptidation of peptidoglycan, not general proteolysis. 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. Supporting Evidence: file:ECOLI/mrdA/mrdA-deep-research-falcon.md PBP2 is a D,D-transpeptidase that forms 4->3 peptide crosslinks |
| GO:0008360 regulation of cell shape | IEA GO_REF:0000043 | ACCEPT | Summary: Core biological function - MrdA/PBP2 is essential for maintaining rod cell shape in E. coli. Reason: Essential and well-documented function. Loss of PBP2 causes cells to become spherical. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Responsible for the determination of the rod shape of the cell |
| GO:0008360 regulation of cell shape | IMP PMID:3894330 Cell shape and division in Escherichia coli: experiments wit... | ACCEPT | Summary: Temperature-sensitive mrdA mutants show loss of rod shape at non-permissive temperature, growing as spherical cells (cocci). Reason: Classic genetic demonstration of PBP2's essential role in cell shape determination. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Temperature-sensitive mutants grow as normal rods at 30 degrees Celsius but grow and divide as cocci during prolonged culturing at 42 degrees Celsius PMID:3894330 Cell shape and division in Escherichia coli: experiments with shape and division mutants. |
| GO:0008360 regulation of cell shape | NAS PMID:31915748 RodZ: a key-player in cell elongation and cell division in E... | ACCEPT | Summary: Review describes PBP2 role in cell shape maintenance as part of the elongasome. Reason: Non-traceable author statement consistent with experimental evidence. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Cell shape PMID:31915748 eCollection 2019. RodZ: a key-player in cell elongation and cell division in Escherichia coli. |
| GO:0008360 regulation of cell shape | IMP PMID:6243629 Cluster of mrdA and mrdB genes responsible for the rod shape... | ACCEPT | Summary: Identification of mrdA gene cluster and demonstration that it controls rod shape and mecillinam sensitivity. Reason: Foundational genetic study identifying mrdA as essential for rod shape. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Responsible for the determination of the rod shape of the cell PMID:6243629 Cluster of mrdA and mrdB genes responsible for the rod shape and mecillinam sensitivity of Escherichia coli. |
| GO:0008360 regulation of cell shape | IMP PMID:1103132 Distinct penicillin binding proteins involved in the divisio... | ACCEPT | Summary: Mutant analysis showing PBP2 is essential for rod shape - mutants that fail to bind beta-lactams to PBP2 grow as round cells. Reason: Classic experimental demonstration of PBP2 role in shape determination. Supporting Evidence: PMID:1103132 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 Constitutive septal murein synthesis in Escherichia coli wit... | ACCEPT | Summary: Impaired PBP2 activity leads to altered morphogenesis and constitutive septal synthesis. Reason: Mutant phenotype demonstrates role in cell shape regulation. Supporting Evidence: file:ECOLI/mrdA/mrdA-uniprot.txt Cell shape PMID:11418550 Constitutive septal murein synthesis in Escherichia coli with impaired activity of the morphogenetic proteins RodA and penicillin-binding protein 2. |
| GO:0046677 response to antibiotic | IMP PMID:1103132 Distinct penicillin binding proteins involved in the divisio... | ACCEPT | 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. 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. Supporting Evidence: PMID:1103132 beta-Lactams that specifically result in the production of ovoid cells bind to penicillin binding protein 2 |
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Download this section (compressed HTML)Q: 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.
Q: 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).
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