{"doi":"10.1107/s2053230x25007034","title":"Crystal structure of a seven-substitution mutant of hydroxynitrile lyase from rubber tree","abstract":"The α/β-hydrolase fold superfamily includes esterases and hydroxynitrile lyases which, despite catalyzing different reactions, share a Ser–His–Asp catalytic triad. We report a 1.99 Å resolution crystal structure of HNL6V, an engineered variant of hydroxynitrile lyase from Hevea brasiliensis ( Hb HNL) containing seven amino-acid substitutions (T11G, E79H, C81L, H103V, N104A, G176S and K236M). The structure reveals that HNL6V maintains the characteristic α/β-hydrolase fold while exhibiting systematic shifts in backbone and catalytic atom positions. Compared with wild-type Hb HNL, the C α positions in HNL6V differ by a mean of 0.2 ± 0.1 Å, representing a statistically significant displacement. Importantly, the catalytic triad and oxyanion-hole atoms have moved 0.2–0.8 Å closer to their corresponding positions in SABP2, although they remain 0.3–1.1 Å from fully achieving the configuration of SABP2. The substitutions also increase local flexibility, particularly in the lid domain covering the active site. This structural characterization demonstrates that targeted amino-acid substitutions can systematically shift catalytic geometries towards those of evolutionarily related enzymes.","journal":"Acta Crystallographica Section F Structural Biology Communications","year":2025,"id":553999,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9083,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":991995,"name":"L. Greenberg","orcid":"0000-0001-6602-2067","position":1,"is_corresponding":false},{"id":1166162,"name":"Meghan E. Walsh","orcid":"0000-0002-9706-7791","position":2,"is_corresponding":false},{"id":103757,"name":"Ke Shi","orcid":"0000-0003-4175-3714","position":3,"is_corresponding":false},{"id":120974,"name":"D. A. Magee","orcid":null,"position":4,"is_corresponding":false},{"id":103759,"name":"Hideki Aihara","orcid":"0000-0001-7508-6230","position":5,"is_corresponding":false},{"id":329591,"name":"Wendy R. Gordon","orcid":"0000-0001-7696-5560","position":6,"is_corresponding":false},{"id":329589,"name":"Robert L. Evans","orcid":"0000-0002-1690-9927","position":7,"is_corresponding":false},{"id":393385,"name":"Romas J. Kazlauskas","orcid":"0000-0002-3570-2411","position":8,"is_corresponding":false},{"id":393383,"name":"Colin T. Pierce","orcid":"0000-0001-9506-9753","position":0,"is_corresponding":true}],"reference_count":27,"raw_metadata":null,"created_at":"2026-07-19T02:54:45.872391Z","pmid":"40864147","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":[]}