{"doi":"10.1111/mmi.12555","title":"Structure of bacteriophage <scp>SPN</scp>1<scp>S</scp> endolysin reveals an unusual two‐module fold for the peptidoglycan lytic and binding activity","abstract":"<jats:title>Summary</jats:title><jats:p>Bacteriophage <jats:styled-content style=\"fixed-case\">SPN</jats:styled-content>1<jats:styled-content style=\"fixed-case\">S</jats:styled-content> infects the pathogenic <jats:styled-content style=\"fixed-case\">G</jats:styled-content>ram‐negative bacterium <jats:styled-content style=\"fixed-case\"><jats:italic>S</jats:italic></jats:styled-content><jats:italic>almonella typhimurium</jats:italic> and expresses endolysin for the release of phage progeny by degrading peptidoglycan of the host cell walls. Bacteriophage <jats:styled-content style=\"fixed-case\">SPN</jats:styled-content>1<jats:styled-content style=\"fixed-case\">S</jats:styled-content> endolysin exhibits high glycosidase activity against peptidoglycans, resulting in antimicrobial activity against a broad range of outer membrane‐permeabilized <jats:styled-content style=\"fixed-case\">G</jats:styled-content>ram‐negative bacteria. Here, we report a crystal structure of <jats:styled-content style=\"fixed-case\">SPN</jats:styled-content>1<jats:styled-content style=\"fixed-case\">S</jats:styled-content> endolysin, indicating that unlike most endolysins from Gram‐negative bacteria background, the α‐helical protein consists of two modular domains, a large and a small domain, with a concave groove between them. Comparison with other structurally homologous glycoside hydrolases indicated a possible peptidoglycan binding site in the groove, and the presence of a catalytic dyad in the vicinity of the groove, one residue in a large domain and the other in a junction between the two domains. The catalytic dyad was further validated by antimicrobial activity assay against outer membrane‐permeabilized <jats:styled-content style=\"fixed-case\"><jats:italic>E</jats:italic></jats:styled-content><jats:italic>scherichia coli</jats:italic>. The three‐helix bundle in the small domain containing a novel class of sequence motif exhibited binding affinity against outer membrane‐permeabilized <jats:styled-content style=\"fixed-case\"><jats:italic>E</jats:italic></jats:styled-content><jats:italic>. coli</jats:italic> and was therefore proposed as the peptidoglycan‐binding domain. These structural and functional features suggest that endolysin from a <jats:styled-content style=\"fixed-case\">G</jats:styled-content>ram‐negative bacterial background has peptidoglycan‐binding activity and performs glycoside hydrolase activity through the catalytic dyad.</jats:p>","journal":"Molecular Microbiology","year":2014,"id":47094,"datarank":1.7854547264694913,"base_score":3.8501476017100584,"endowment":3.8501476017100584,"self_citation_contribution":0.5775221402565088,"citation_network_contribution":1.2079325862129826,"self_endowment_contribution":0.5775221402565088,"citer_contribution":1.2079325862129826,"corpus_percentile":null,"corpus_rank":null,"citation_count":46,"citer_count":43,"citers_with_citation_signal":35,"citers_with_endowment":35,"datacite_reuse_total":2,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":217478,"name":"Jeong‐A. Lim","orcid":null,"position":1,"is_corresponding":false},{"id":217480,"name":"Minsuk Kong","orcid":null,"position":2,"is_corresponding":false},{"id":217482,"name":"Sangryeol Ryu","orcid":null,"position":3,"is_corresponding":false},{"id":217483,"name":"Sangkee Rhee","orcid":null,"position":4,"is_corresponding":false},{"id":217474,"name":"Yangshin Park","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Structure of bacteriophage <scp>SPN</scp>1<scp>S</scp> endolysin reveals an unusual two‐module fold for the peptidoglycan lytic and binding activity","abstract":"<jats:title>Summary</jats:title><jats:p>Bacteriophage <jats:styled-content style=\"fixed-case\">SPN</jats:styled-content>1<jats:styled-content style=\"fixed-case\">S</jats:styled-content> infects the pathogenic <jats:styled-content style=\"fixed-case\">G</jats:styled-content>ram‐negative bacterium <jats:styled-content style=\"fixed-case\"><jats:italic>S</jats:italic></jats:styled-content><jats:italic>almonella typhimurium</jats:italic> and expresses endolysin for the release of phage progeny by degrading peptidoglycan of the host cell walls. Bacteriophage <jats:styled-content style=\"fixed-case\">SPN</jats:styled-content>1<jats:styled-content style=\"fixed-case\">S</jats:styled-content> endolysin exhibits high glycosidase activity against peptidoglycans, resulting in antimicrobial activity against a broad range of outer membrane‐permeabilized <jats:styled-content style=\"fixed-case\">G</jats:styled-content>ram‐negative bacteria. Here, we report a crystal structure of <jats:styled-content style=\"fixed-case\">SPN</jats:styled-content>1<jats:styled-content style=\"fixed-case\">S</jats:styled-content> endolysin, indicating that unlike most endolysins from Gram‐negative bacteria background, the α‐helical protein consists of two modular domains, a large and a small domain, with a concave groove between them. Comparison with other structurally homologous glycoside hydrolases indicated a possible peptidoglycan binding site in the groove, and the presence of a catalytic dyad in the vicinity of the groove, one residue in a large domain and the other in a junction between the two domains. The catalytic dyad was further validated by antimicrobial activity assay against outer membrane‐permeabilized <jats:styled-content style=\"fixed-case\"><jats:italic>E</jats:italic></jats:styled-content><jats:italic>scherichia coli</jats:italic>. The three‐helix bundle in the small domain containing a novel class of sequence motif exhibited binding affinity against outer membrane‐permeabilized <jats:styled-content style=\"fixed-case\"><jats:italic>E</jats:italic></jats:styled-content><jats:italic>. coli</jats:italic> and was therefore proposed as the peptidoglycan‐binding domain. These structural and functional features suggest that endolysin from a <jats:styled-content style=\"fixed-case\">G</jats:styled-content>ram‐negative bacterial background has peptidoglycan‐binding activity and performs glycoside hydrolase activity through the catalytic dyad.</jats:p>","is_dataset_classified":null,"base_score":3.8501476017100584,"endowment":3.8501476017100584,"datacite_reuse_total":2,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"24641441","pmcid":null,"openalex_id":"https://openalex.org/W2158616732","authors":[],"funders":[],"total_grants":0,"fwci":2.1207,"citation_percentile":0.86869052,"influential_citations":4,"citation_trend":[{"year":2015,"count":3},{"year":2017,"count":4},{"year":2018,"count":1},{"year":2019,"count":1},{"year":2020,"count":4},{"year":2021,"count":7},{"year":2022,"count":4},{"year":2023,"count":4},{"year":2024,"count":6},{"year":2025,"count":8},{"year":2026,"count":4}],"oa_status":"closed","license":"http://onlinelibrary.wiley.com/termsAndConditions#vor","oa_locations":[{"url":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmmi.12555","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/mmi.12555","host_type":"publisher"},{"url":"https://doi.org/10.1111/mmi.12555","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/24641441","host_type":"repository"}],"fields_of_study":["Bacteriophages and microbial interactions","RNA and protein synthesis mechanisms","Genomics and Phylogenetic Studies","Biology","Medicine","Chemistry","Materials Science","Binding Sites","Crystallography, X-Ray","Endopeptidases","Escherichia coli","Glycoside Hydrolases","Hydrolysis","Models, Molecular","Peptidoglycan","Protein Binding","Protein Structure, Tertiary","Salmonella Phages","Salmonella typhimurium"],"mesh_terms":["Binding Sites","Escherichia coli","Glycoside Hydrolases","Hydrolysis","Models, Molecular","Endopeptidases","Peptidoglycan","Protein Binding","Salmonella Phages","Salmonella typhimurium","Protein Structure, Tertiary","Crystallography, X-Ray"],"keywords":["Lysin","Peptidoglycan","Biology","Bacteriophage","Lytic cycle","Biochemistry","Bacterial outer membrane","Bacterial cell structure","Cell wall","Bacteria","Biophysics","Escherichia coli","Genetics"],"sdg_mappings":[],"linked_datasets":[{"doi":"10.6084/m9.figshare.19759419.v1","title":"Additional file 1 of A myxobacterial GH19 lysozyme with bacteriolytic activity on both Gram-positive and negative phytopathogens","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.19759419","title":"Additional file 1 of A myxobacterial GH19 lysozyme with bacteriolytic activity on both Gram-positive and negative phytopathogens","publisher":"figshare","resource_type":"JournalArticle"}],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-16T23:54:33.851900Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}