| Citation (PMID/DOI) | Evidence Type | Supports/Refutes/Qualifies | Claim Tested | Key Finding | Organism/Assay Context | Confidence and Limitations |
|---|---|---|---|---|---|---|
| Zinkle et al. 2025, Nature Communications, doi:10.1038/s41467-025-65515-3 | Structural/evolutionary; cryo-EM | Qualifies | Does MCR-1 directly have GO:0016776, and what is its specific chemistry? | Full-length MCR-1 structure shows PE donor bound near active site and lipid A bound ~20 Å away in TM region; catalytic cycle transfers phosphoethanolamine (PEtN) to the 4'-phosphate of lipid A via T285 intermediate. This supports a phosphate-group acceptor reaction at a broad level but identifies the specific activity as lipid A phosphoethanolamine transferase, making GO:0016776 too general. (pqac-00000001, pqac-00000005, pqac-00000026, pqac-00000028) | MCR-1 structural and mechanistic analysis; ligand-bound cryo-EM and functional interpretation | High confidence for mechanism and acceptor identity; publication year 2025 is beyond the user's preferred 2023-2024 window but is highly informative. |
| Sun & Palzkill 2021, mBio, doi:10.1128/mBio.02776-21 | Direct assay + mutational scanning | Supports | Is MCR-1 an active enzyme rather than a pseudo-enzyme, and what residues are essential? | Deep mutational scanning of 23 active-site positions found 17 strongly constrained for function; T285 is catalytic nucleophile, and substitutions at T285, E246, D465 and other active-site residues markedly reduce activity/resistance. Confirms intact catalytic machinery and active PEtN transferase function. (pqac-00000000, pqac-00000002, pqac-00000004, pqac-00000006, pqac-00000019, pqac-00000020, pqac-00000030) | E. coli expressing MCR-1; polymyxin selection, deep sequencing, in vitro/in vivo functional analyses | High confidence for essential residue mapping; does not itself define the most specific GO term. |
| Thai et al. 2023, Antibiotics, doi:10.3390/antibiotics12091382 | Review/database synthesis | Qualifies | Is GO:0016776 the best functional annotation, and what is the catalytic mechanism? | Summarizes Class I PEA transferase mechanism: MCR-1 uses Zn2+-dependent ping-pong catalysis to transfer PEtN from PE to lipid A phosphate groups, with key residues Thr285, Glu246, His466 and others. Supports broad phosphotransferase classification but emphasizes a more specific phosphoethanolamine transferase activity. (pqac-00000003, pqac-00000007, pqac-00000013, pqac-00000016, pqac-00000018, pqac-00000022, pqac-00000027, pqac-00000031, pqac-00000032) | Cross-species structural/biochemical synthesis of pathogenic Gram-negative PETs | Moderate-high confidence; review rather than primary assay, but integrates multiple structural and biochemical studies. |
| Anandan et al. 2017, PNAS, doi:10.1073/pnas.1612927114 | Structural/evolutionary | Qualifies | What is the closest characterized homolog/subfamily, and could TreeGrafter have propagated a family-level term? | Full-length NmEptA structure establishes canonical Class I lipid A phosphoethanolamine transferase architecture in the alkaline phosphatase superfamily. MCR-1 is placed in this same subfamily rather than a generic phosphotransferase bucket. Supports nearest characterized homolog assignment to EptA-like lipid A PETs. (pqac-00000014, pqac-00000025) | Neisseria meningitidis EptA full-length crystal structure | High confidence for subfamily placement; homolog is not MCR-1 itself, so chemistry is inferred by homology plus later MCR-1 work. |
| Samantha & Vrielink 2020, J Mol Biol, doi:10.1016/j.jmb.2020.04.022 | Review/structural synthesis | Qualifies | Are MCR-1 catalytic residues and fold consistent with active lipid A PET enzymes? | Reviews strong structural/mechanistic congruence between MCR-1 and EptA, including conserved metal-binding residues and catalytic threonine; identifies lipid A phosphate headgroups as acceptor sites and MCR proteins as plasmid-borne EptA-like enzymes. (pqac-00000011, pqac-00000012, pqac-00000017, pqac-00000029) | Comparative structural biology of lipid A PETs | High confidence for conserved mechanism; review-level evidence, not a dedicated MCR-1 assay. |
| Schumann et al. 2024, Microbiol Mol Biol Rev, doi:10.1128/mmbr.00193-23 | Review/evolutionary analysis | Qualifies | Is MCR-1 correctly placed within the lipid A-modifying PET clade rather than another alkaline phosphatase-superfamily neighbor? | Distinguishes three PET clades: lipid A-modifying eptA/mcr, KDO-modifying eptB, and inner-core-modifying cptA/eptC. Supports that MCR-1 belongs specifically to the lipid A-modifying PET clade and likely evolved from chromosomal eptA-like ancestors. (pqac-00000015) | Broad comparative review of PET diversity and function | Moderate-high confidence; useful for mis-placement testing, but mostly comparative and not direct biochemical assay of MCR-1. |
| Schumann et al. 2024, mSphere, doi:10.1128/msphere.00731-24 | Direct assay/comparative functional study | Qualifies | Is MCR-1 merely generic lipid A PET activity, or a more specific site-selective subfamily function? | In isogenic E. coli, MCR-1 selectively modifies the 4'-phosphate of lipid A, unlike EptA and MCR-9 which prefer the 1-phosphate. This refines function below the broad GO:0016776 level and shows subfamily-specific acceptor-site selectivity. (pqac-00000015) | Isogenic E. coli expression system; MALDI/phenotype comparisons among PETs | High confidence for site-selectivity; recent and directly relevant, though citation context available here is summarized via review retrieval. |
| Anderson et al. 2020, J Biol Chem, doi:10.1074/jbc.RA119.011668 | Structural/evolutionary | Competing/qualifies | Could MCR-1 be mis-assigned within the alkaline phosphatase superfamily to a different neighboring subfamily? | BcsG is also a Zn2+-dependent phosphoethanolamine transferase in the alkaline phosphatase superfamily, but acts on cellulose rather than lipid A. This demonstrates that superfamily membership alone is insufficient; substrate-specific subfamily placement is essential. MCR-1 is therefore not just any alkaline-phosphatase-like phosphotransferase. (pqac-00000024) | E. coli BcsG structural and functional characterization | Moderate confidence for warning against within-superfamily overgeneralization; indirect evidence for MCR-1. |
| Liu et al. 2017, Antimicrob Agents Chemother, doi:10.1128/AAC.00580-17 | Direct assay/chemical analysis | Supports | Does MCR-1 directly modify lipid A with PEtN in vivo? | Mass spectrometric analysis showed MCR-1 causes phosphoethanolamine modification of lipid A in Gram-negative pathogens. This directly supports the specific biochemical role of MCR-1 as a lipid A phosphoethanolamine transferase. (pqac-00000000) | Gram-negative ESKAPE pathogens; lipid A structural analysis by mass spectrometry | High confidence for product identification; does not map all catalytic residues. |
| Gaballa et al. 2023, Front Cell Infect Microbiol, doi:10.3389/fcimb.2023.1060519 | Evolutionary/computational | Qualifies | Can sequence similarity alone justify GO:0016776 propagation to MCR-1? | Large-scale phylogeny of mcr-like and intrinsic PET genes found sequence similarity alone is insufficient to discriminate colistin-resistance PETs from other intrinsic lipid-modification PETs. Supports caution with TreeGrafter family-level propagation and argues for subfamily-aware curation. (pqac-00000015) | Comparative genomics/phylogeny across thousands of PET homologs | Moderate confidence; powerful for annotation caution, but not a direct enzymology study. |
| Purcell et al. 2022, J Bacteriol, doi:10.1128/JB.00498-21 | Functional genetics/physiology | Supports | Is MCR-1 an active PE-dependent lipid A PET in cells? | DgkA is required for polymyxin resistance mediated by MCR-1 and other lipid A PEtN transferases because PE donor usage generates DAG that must be recycled. This provides orthogonal physiological support for the PE-to-lipid A phosphoethanolamine transfer mechanism. (pqac-00000003) | E. coli genetics; dgkA deletion and polymyxin-resistance phenotyping | Moderate-high confidence; indirect for active-site chemistry but directly consistent with donor/product logic. |


*Table: This table summarizes the key primary and review evidence used to judge whether MCR-1 should carry the broad GO:0016776 annotation. It highlights that MCR-1 is an active lipid A phosphoethanolamine transferase, so the propagated term is best treated as broadly true but too general.*