{"id":"https://openalex.org/W2783374433","doi":"https://doi.org/10.1042/bcj20170838","title":"Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen, Fusobacterium nucleatum","display_name":"Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen, Fusobacterium nucleatum","publication_year":2018,"publication_date":"2018-01-18","ids":{"openalex":"https://openalex.org/W2783374433","doi":"https://doi.org/10.1042/bcj20170838","mag":"2783374433","pmid":"https://pubmed.ncbi.nlm.nih.gov/29343611"},"language":"en","primary_location":{"id":"doi:10.1042/bcj20170838","doi":"https://doi.org/10.1042/bcj20170838","is_oa":false,"landing_page_url":"https://doi.org/10.1042/bcj20170838","pdf_url":null,"source":{"id":"https://openalex.org/S44425019","display_name":"Biochemical Journal","issn_l":"0264-6021","issn":["0264-6021","1470-8728"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","doyens","jufo-2","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310311608","host_organization_name":"Portland Press","host_organization_lineage":["https://openalex.org/P4310311608","https://openalex.org/P4310311715"],"host_organization_lineage_names":["Portland Press","Biochemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biochemical Journal","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081481910","display_name":"Yuichiro Kezuka","orcid":"https://orcid.org/0000-0003-4039-3825","observed_orcids":["https://orcid.org/0000-0003-4039-3825"]},"institutions":[{"id":"https://openalex.org/I180680657","display_name":"Iwate Medical University","ror":"https://ror.org/04cybtr86","country_code":"JP","type":"education","lineage":["https://openalex.org/I180680657"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yuichiro Kezuka","raw_affiliation_strings":["Department of Structural Biology, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Structural Biology, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan","institution_ids":["https://openalex.org/I180680657"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103429842","display_name":"Tetsuo Ishida","orcid":"https://orcid.org/0009-0009-5150-9433","observed_orcids":["https://orcid.org/0009-0009-5150-9433"]},"institutions":[{"id":"https://openalex.org/I32915989","display_name":"University of the Ryukyus","ror":"https://ror.org/02z1n9q24","country_code":"JP","type":"education","lineage":["https://openalex.org/I32915989"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tetsuo Ishida","raw_affiliation_strings":["Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan","institution_ids":["https://openalex.org/I32915989"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101878350","display_name":"Yasuo Yoshida","orcid":"https://orcid.org/0000-0001-5943-7002","observed_orcids":["https://orcid.org/0000-0001-5943-7002"]},"institutions":[{"id":"https://openalex.org/I195444995","display_name":"Aichi Gakuin University","ror":"https://ror.org/01rwx7470","country_code":"JP","type":"education","lineage":["https://openalex.org/I195444995"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasuo Yoshida","raw_affiliation_strings":["Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Aichi 452-8650, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Aichi 452-8650, Japan","institution_ids":["https://openalex.org/I195444995"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015523164","display_name":"Takamasa Nonaka","orcid":"https://orcid.org/0000-0001-6967-9574","observed_orcids":["https://orcid.org/0000-0001-6967-9574"]},"institutions":[{"id":"https://openalex.org/I180680657","display_name":"Iwate Medical University","ror":"https://ror.org/04cybtr86","country_code":"JP","type":"education","lineage":["https://openalex.org/I180680657"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takamasa Nonaka","raw_affiliation_strings":["Department of Structural Biology, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Structural Biology, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan","institution_ids":["https://openalex.org/I180680657"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5081481910"],"corresponding_institution_ids":["https://openalex.org/I180680657"],"apc_list":null,"apc_paid":null,"fwci":0.5672,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.67471144,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"475","issue":"4","first_page":"733","last_page":"748"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.5067999958992004,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.5067999958992004,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11481","display_name":"Sulfur Compounds in Biology","score":0.2915000021457672,"subfield":{"id":"https://openalex.org/subfields/1303","display_name":"Biochemistry"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12770","display_name":"Amino Acid Enzymes and Metabolism","score":0.05009999871253967,"subfield":{"id":"https://openalex.org/subfields/1303","display_name":"Biochemistry"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fusobacterium-nucleatum","display_name":"Fusobacterium nucleatum","score":0.921999990940094},{"id":"https://openalex.org/keywords/hydrogen-sulfide-production","display_name":"hydrogen sulfide production","score":0.8299999833106995},{"id":"https://openalex.org/keywords/pyridoxal-phosphate-dependent-enzymes","display_name":"pyridoxal phosphate-dependent enzymes","score":0.9020000100135803},{"id":"https://openalex.org/keywords/cysteine","display_name":"cysteine","score":0.7110000252723694},{"id":"https://openalex.org/keywords/l-serine","display_name":"L-serine","score":0.9210000038146973},{"id":"https://openalex.org/keywords/schiff-base","display_name":"Schiff base","score":0.6309999823570251},{"id":"https://openalex.org/keywords/water-addition","display_name":"water addition","score":0.6710000038146973},{"id":"https://openalex.org/keywords/periodontitis","display_name":"periodontitis","score":0.6859999895095825},{"id":"https://openalex.org/keywords/oral-pathogens","display_name":"oral pathogens","score":0.5740000009536743},{"id":"https://openalex.org/keywords/enzyme-mechanism","display_name":"enzyme mechanism","score":0.5910000205039978},{"id":"https://openalex.org/keywords/stopped-flow-kinetics","display_name":"stopped-flow kinetics","score":0.5680000185966492}],"concepts":[{"id":"https://openalex.org/C2777269803","wikidata":"https://www.wikidata.org/wiki/Q407727","display_name":"Lyase","level":3,"score":0.7893044352531433},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7702745199203491},{"id":"https://openalex.org/C2779201268","wikidata":"https://www.wikidata.org/wiki/Q186474","display_name":"Cysteine","level":3,"score":0.7223941087722778},{"id":"https://openalex.org/C2777349128","wikidata":"https://www.wikidata.org/wiki/Q5510311","display_name":"Fusobacterium nucleatum","level":4,"score":0.6211525201797485},{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.6035144925117493},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.5972074270248413},{"id":"https://openalex.org/C2776428424","wikidata":"https://www.wikidata.org/wiki/Q2602701","display_name":"Schiff base","level":2,"score":0.52037113904953},{"id":"https://openalex.org/C2776414213","wikidata":"https://www.wikidata.org/wiki/Q183290","display_name":"Serine","level":3,"score":0.4963088631629944},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3196384310722351},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.2949153184890747},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.26558610796928406},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.084771066904068},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08140984177589417},{"id":"https://openalex.org/C2780183776","wikidata":"https://www.wikidata.org/wiki/Q3214147","display_name":"Porphyromonas gingivalis","level":3,"score":0.0651068389415741},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D003547","descriptor_name":"Cysteine Synthase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003547","descriptor_name":"Cysteine Synthase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003547","descriptor_name":"Cysteine Synthase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006862","descriptor_name":"Hydrogen Sulfide","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006862","descriptor_name":"Hydrogen Sulfide","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012545","descriptor_name":"Schiff Bases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016967","descriptor_name":"Fusobacterium nucleatum","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":true},{"descriptor_ui":"D016967","descriptor_name":"Fusobacterium nucleatum","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D017665","descriptor_name":"Hydroxyl Radical","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1042/bcj20170838","doi":"https://doi.org/10.1042/bcj20170838","is_oa":false,"landing_page_url":"https://doi.org/10.1042/bcj20170838","pdf_url":null,"source":{"id":"https://openalex.org/S44425019","display_name":"Biochemical Journal","issn_l":"0264-6021","issn":["0264-6021","1470-8728"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","doyens","jufo-2","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310311608","host_organization_name":"Portland Press","host_organization_lineage":["https://openalex.org/P4310311608","https://openalex.org/P4310311715"],"host_organization_lineage_names":["Portland Press","Biochemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biochemical Journal","raw_type":"journal-article"},{"id":"pmid:29343611","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29343611","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Biochemical journal","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2481889558","display_name":"Searching and improvement of the compounds that prevent production of odorous and toxic substances produced by periodontal pathogens","funder_award_id":"16K11485","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1488975476","https://openalex.org/W1542637321","https://openalex.org/W1622552814","https://openalex.org/W1766949951","https://openalex.org/W1963947860","https://openalex.org/W1975531605","https://openalex.org/W1980897706","https://openalex.org/W1999728411","https://openalex.org/W2005980540","https://openalex.org/W2006922696","https://openalex.org/W2013901882","https://openalex.org/W2019825242","https://openalex.org/W2021847541","https://openalex.org/W2038840577","https://openalex.org/W2040362276","https://openalex.org/W2042670525","https://openalex.org/W2044747464","https://openalex.org/W2056549125","https://openalex.org/W2065283382","https://openalex.org/W2065362549","https://openalex.org/W2066186053","https://openalex.org/W2074986801","https://openalex.org/W2076467936","https://openalex.org/W2077400653","https://openalex.org/W2088623675","https://openalex.org/W2095789085","https://openalex.org/W2096064309","https://openalex.org/W2097493124","https://openalex.org/W2098262530","https://openalex.org/W2108593861","https://openalex.org/W2116308401","https://openalex.org/W2122160767","https://openalex.org/W2129749735","https://openalex.org/W2131765423","https://openalex.org/W2131942711","https://openalex.org/W2132629607","https://openalex.org/W2144081223","https://openalex.org/W2147322234","https://openalex.org/W2147576307","https://openalex.org/W2152448366","https://openalex.org/W2155344685","https://openalex.org/W2165011009","https://openalex.org/W2529991396","https://openalex.org/W2950288866","https://openalex.org/W4302343761"],"related_works":["https://openalex.org/W2559221575","https://openalex.org/W2967072854","https://openalex.org/W2147322234","https://openalex.org/W2075812583","https://openalex.org/W2129749735","https://openalex.org/W2122160767","https://openalex.org/W3128312199","https://openalex.org/W4386101783","https://openalex.org/W3095002150","https://openalex.org/W2141014820"],"abstract_inverted_index":{"Hydrogen":[0],"sulfide":[1],"(H2S)":[2],"plays":[3],"important":[4],"roles":[5],"in":[6,18,118,129,139,239],"the":[7,41,61,64,79,85,96,130,135,140,149,154,158,170,174,185,212,222,236],"pathogenesis":[8],"of":[9,43,67,78,122,132,151,169,193,221,235],"periodontitis.":[10],"Oral":[11],"pathogens":[12],"typically":[13],"produce":[14,157],"H2S":[15,44],"from":[16,26,47],"l-cysteine":[17,48,133],"addition":[19,150,180],"to":[20,109,114,153,156,233],"pyruvate":[21],"and":[22,45,49,93,95,102,111,199,214],".":[23],"However,":[24],"fn1055":[25],"Fusobacterium":[27],"nucleatum":[28,30],"subsp.":[29],"ATCC":[31],"25586":[32],"encodes":[33],"a":[34,76,106,219],"pyridoxal":[35],"5\u2032-phosphate":[36],"(PLP)-dependent":[37],"enzyme":[38],"that":[39,84,144,178],"catalyzes":[40],"production":[42],"l-serine":[46],"H2O,":[50],"an":[51,167],"unusual":[52],"cysteine":[53,223],"(hydroxyl)":[54,224],"lyase":[55,225],"reaction":[56,62,175,226],"(\u03b2-replacement":[57],"reaction).":[58],"To":[59],"reveal":[60],"mechanism,":[63],"crystal":[65],"structure":[66,127],"substrate-free":[68],"Fn1055":[69,110],"was":[70],"determined.":[71],"Based":[72],"on":[73,211],"this":[74],"structure,":[75],"model":[77],"l-cysteine-PLP":[80],"Schiff":[81,137,160],"base":[82,138],"suggested":[83],"thiol":[86],"group":[87],"forms":[88],"hydrogen":[89],"bonds":[90],"with":[91,100],"Asp232":[92,104,145,183],"Ser74,":[94],"substrate":[97],"\u03b1-carboxylate":[98],"interacts":[99],"Thr73":[101],"Gln147.":[103],"is":[105,146,184],"unique":[107],"residue":[108],"its":[112],"substitution":[113],"asparagine":[115],"(D232N)":[116],"resulted":[117],"almost":[119],"complete":[120],"loss":[121],"\u03b2-replacement":[123,203],"activity.":[124],"The":[125,229],"D232N":[126],"obtained":[128],"presence":[131],"contained":[134],"\u03b1-aminoacrylate-PLP":[136],"active":[141],"site,":[142],"indicating":[143],"essential":[147],"for":[148],"water":[152,179],"\u03b1-aminoacrylate":[155,171],"l-serine-PLP":[159],"base.":[161],"Rapid-scan":[162],"stopped-flow":[163],"kinetic":[164],"analyses":[165],"showed":[166],"accumulation":[168],"intermediate":[172],"during":[173],"cycle,":[176],"suggesting":[177],"mediated":[181],"by":[182,205,227],"rate-limiting":[186],"step.":[187],"In":[188],"contrast,":[189],"mutants":[190],"containing":[191],"substitutions":[192],"other":[194],"active-site":[195],"residues":[196],"(Ser74,":[197],"Thr73,":[198],"Gln147)":[200],"exhibited":[201],"reduced":[202],"activity":[204],"more":[206],"than":[207],"100-fold.":[208],"Finally,":[209],"based":[210],"structural":[213],"biochemical":[215],"analyses,":[216],"we":[217],"propose":[218],"mechanism":[220,238],"Fn1055.":[228],"present":[230],"study":[231],"leads":[232],"elucidation":[234],"H2S-producing":[237],"F.":[240],"nucleatum.":[241]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2018-01-26T00:00:00"}