{"id":"https://openalex.org/W2090160089","doi":"https://doi.org/10.1002/(sici)1097-0282(199909)50:3<319::aid-bip7>3.0.co;2-8","title":"Docking of 4-oxalocrotonate tautomerase substrates: Implications for the catalytic mechanism","display_name":"Docking of 4-oxalocrotonate tautomerase substrates: Implications for the catalytic mechanism","publication_year":1999,"publication_date":"1999-09-01","ids":{"openalex":"https://openalex.org/W2090160089","doi":"https://doi.org/10.1002/(sici)1097-0282(199909)50:3<319::aid-bip7>3.0.co;2-8","mag":"2090160089","pmid":"https://pubmed.ncbi.nlm.nih.gov/10397792"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1097-0282(199909)50:3<319::aid-bip7>3.0.co;2-8","doi":"https://doi.org/10.1002/(sici)1097-0282(199909)50:3<319::aid-bip7>3.0.co;2-8","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1097-0282(199909)50:3<319::aid-bip7>3.0.co;2-8","pdf_url":null,"source":{"id":"https://openalex.org/S56808608","display_name":"Biopolymers","issn_l":"0006-3525","issn":["0006-3525","1097-0282"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biopolymers","raw_type":"journal-article"},"volume":null,"type":"article","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/A5086065566","display_name":"Thereza A. Soares","orcid":"https://orcid.org/0000-0002-5891-6906","observed_orcids":["https://orcid.org/0000-0002-5891-6906"]},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]},{"id":"https://openalex.org/I25112270","display_name":"Universidade Federal de Pernambuco","ror":"https://ror.org/047908t24","country_code":"BR","type":"education","lineage":["https://openalex.org/I25112270"]}],"countries":["BR","US"],"is_corresponding":false,"raw_author_name":"T. A. Soares","raw_affiliation_strings":["Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA","Departamento de Quimica Fundamental, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I123431417"]},{"raw_affiliation_string":"Departamento de Quimica Fundamental, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil","institution_ids":["https://openalex.org/I25112270"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040337866","display_name":"David S. Goodsell","orcid":"https://orcid.org/0000-0002-5932-2130","observed_orcids":["https://orcid.org/0000-0002-5932-2130"]},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. S. Goodsell","raw_affiliation_strings":["Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062602935","display_name":"James M. Briggs","orcid":"https://orcid.org/0000-0001-5863-8945","observed_orcids":["https://orcid.org/0000-0001-5863-8945"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. M. Briggs","raw_affiliation_strings":["Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":null,"display_name":"R. Ferreira","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I25112270","display_name":"Universidade Federal de Pernambuco","ror":"https://ror.org/047908t24","country_code":"BR","type":"education","lineage":["https://openalex.org/I25112270"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["BR","US"],"is_corresponding":false,"raw_author_name":"R. Ferreira","raw_affiliation_strings":["Departamento de Quimica Fundamental, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil","Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Quimica Fundamental, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil","institution_ids":["https://openalex.org/I25112270"]},{"raw_affiliation_string":"Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058956938","display_name":"Arthur J. Olson","orcid":"https://orcid.org/0000-0003-0558-4618","observed_orcids":["https://orcid.org/0000-0003-0558-4618"]},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A. J. Olson","raw_affiliation_strings":["Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I123431417"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5058956938"],"corresponding_institution_ids":["https://openalex.org/I123431417"],"apc_list":{"value":4150,"currency":"USD","value_usd":4150},"apc_paid":null,"fwci":0.343,"has_fulltext":false,"cited_by_count":30,"citation_normalized_percentile":{"value":0.54608839,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"50","issue":"3","first_page":"319","last_page":"328"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.454800009727478,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular 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/T10044","display_name":"Protein Structure and Dynamics","score":0.454800009727478,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular 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/T12191","display_name":"Chemical Reaction Mechanisms","score":0.2655999958515167,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.22059999406337738,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/4-oxalocrotonate-tautomerase","display_name":"4-oxalocrotonate tautomerase","score":0.996999979019165},{"id":"https://openalex.org/keywords/substrate-binding","display_name":"substrate binding","score":0.4620000123977661},{"id":"https://openalex.org/keywords/molecular-docking","display_name":"molecular docking","score":0.6470000147819519},{"id":"https://openalex.org/keywords/catalytic-mechanism","display_name":"catalytic mechanism","score":0.7889999747276306},{"id":"https://openalex.org/keywords/general-acid-base-catalysis","display_name":"general acid-base catalysis","score":0.8529999852180481},{"id":"https://openalex.org/keywords/pka-prediction","display_name":"pKa prediction","score":0.7409999966621399},{"id":"https://openalex.org/keywords/krebs-cycle-intermediates","display_name":"Krebs cycle intermediates","score":0.9150000214576721}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.9054464101791382},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7155583500862122},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.66917484998703},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.662886381149292},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.5740948915481567},{"id":"https://openalex.org/C63338738","wikidata":"https://www.wikidata.org/wiki/Q287862","display_name":"Catalytic cycle","level":3,"score":0.5234022736549377},{"id":"https://openalex.org/C69118441","wikidata":"https://www.wikidata.org/wiki/Q2941663","display_name":"Enzyme catalysis","level":3,"score":0.506076991558075},{"id":"https://openalex.org/C2779815552","wikidata":"https://www.wikidata.org/wiki/Q484583","display_name":"Proline","level":3,"score":0.4747479557991028},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.427510142326355},{"id":"https://openalex.org/C2993359049","wikidata":"https://www.wikidata.org/wiki/Q7575016","display_name":"Catalytic efficiency","level":3,"score":0.42169415950775146},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.38104164600372314},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.3705233931541443},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.35885077714920044},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000447","descriptor_name":"Aldehydes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007535","descriptor_name":"Isomerases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013011","descriptor_name":"Sorbic Acid","qualifier_ui":"Q000031","qualifier_name":"analogs & derivatives","is_major_topic":true},{"descriptor_ui":"D013011","descriptor_name":"Sorbic Acid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016958","descriptor_name":"Pseudomonas putida","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1002/(sici)1097-0282(199909)50:3<319::aid-bip7>3.0.co;2-8","doi":"https://doi.org/10.1002/(sici)1097-0282(199909)50:3<319::aid-bip7>3.0.co;2-8","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1097-0282(199909)50:3<319::aid-bip7>3.0.co;2-8","pdf_url":null,"source":{"id":"https://openalex.org/S56808608","display_name":"Biopolymers","issn_l":"0006-3525","issn":["0006-3525","1097-0282"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biopolymers","raw_type":"journal-article"},{"id":"pmid:10397792","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/10397792","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":"Biopolymers","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3249601790","display_name":"Drug Design Cycle targeting HIV Protease Drug Resistance","funder_award_id":"P01GM048870","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W93588716","https://openalex.org/W1583292915","https://openalex.org/W1966735171","https://openalex.org/W1969518814","https://openalex.org/W1972925411","https://openalex.org/W1979046104","https://openalex.org/W2000297152","https://openalex.org/W2009432607","https://openalex.org/W2024243556","https://openalex.org/W2026569411","https://openalex.org/W2034774678","https://openalex.org/W2039665613","https://openalex.org/W2040816544","https://openalex.org/W2050433824","https://openalex.org/W2051163038","https://openalex.org/W2057406332","https://openalex.org/W2075662564","https://openalex.org/W2076123583","https://openalex.org/W2076412028","https://openalex.org/W2079243965","https://openalex.org/W2080653934","https://openalex.org/W2093166740","https://openalex.org/W2123859926","https://openalex.org/W2125097802","https://openalex.org/W2139508887","https://openalex.org/W2149653798","https://openalex.org/W2156160283","https://openalex.org/W2158534713","https://openalex.org/W2314118227","https://openalex.org/W2332112743","https://openalex.org/W2488677743","https://openalex.org/W3047550486","https://openalex.org/W4247951394"],"related_works":["https://openalex.org/W2004741748","https://openalex.org/W2030628697","https://openalex.org/W2011685425","https://openalex.org/W2000297152","https://openalex.org/W2058852594","https://openalex.org/W1969466983","https://openalex.org/W1999767410","https://openalex.org/W2012822298","https://openalex.org/W2011196844","https://openalex.org/W2091465930"],"abstract_inverted_index":{"The":[0,19,76,110],"enzyme":[1,20,106,125],"4-oxalocrotonate":[2,59],"tautomerase":[3,60],"catalyzes":[4],"the":[5,16,29,38,47,52,73,91,100,105,120,124],"ketonization":[6],"of":[7,54,58,80,94,104],"dienols,":[8],"which":[9,98],"after":[10],"further":[11],"processing":[12],"become":[13],"intermediates":[14],"in":[15,83],"Krebs":[17],"cycle.":[18],"uses":[21],"a":[22],"general":[23,121],"acid-base":[24],"mechanism":[25],"for":[26,72,90,123],"proton":[27],"transfer:":[28],"amino-terminal":[30],"proline":[31],"has":[32,43],"been":[33,44],"shown":[34],"to":[35],"function":[36],"as":[37,46,119],"catalytic":[39,48,102],"base":[40],"and":[41,65,113],"Arg39":[42,118],"implicated":[45],"acid.":[49],"We":[50],"report":[51],"results":[53],"molecular":[55],"docking":[56,114],"simulations":[57,115],"with":[61,85],"two":[62],"substrates,":[63],"2-hydroxymuconate":[64,81],"5-carboxymethyl-2-hydroxymuconate.":[66],"pKa":[67,111],"calculations":[68],"are":[69],"also":[70],"performed":[71],"free":[74],"enzyme.":[75],"predicted":[77],"binding":[78,92],"mode":[79,93],"is":[82,96],"agreement":[84],"experimental":[86],"data.":[87],"A":[88],"model":[89],"5-carboxymethyl-2-hydroxymuconate":[95],"proposed":[97],"explains":[99],"lower":[101],"efficiency":[103],"toward":[107],"this":[108],"substrate.":[109],"predictions":[112],"support":[116],"residue":[117],"acid":[122],"catalysis.":[126]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-11-01T11:40:01.658920","created_date":"2016-06-24T00:00:00"}
