{"id":"https://openalex.org/W1973010540","doi":"https://doi.org/10.1021/bi00033a004","title":"Human Alanyl-tRNA Synthetase: Conservation in Evolution of Catalytic Core and Microhelix Recognition","display_name":"Human Alanyl-tRNA Synthetase: Conservation in Evolution of Catalytic Core and Microhelix Recognition","publication_year":1995,"publication_date":"1995-08-22","ids":{"openalex":"https://openalex.org/W1973010540","doi":"https://doi.org/10.1021/bi00033a004","mag":"1973010540","pmid":"https://pubmed.ncbi.nlm.nih.gov/7654687"},"language":"en","primary_location":{"id":"doi:10.1021/bi00033a004","doi":"https://doi.org/10.1021/bi00033a004","is_oa":false,"landing_page_url":"https://doi.org/10.1021/bi00033a004","pdf_url":null,"source":{"id":"https://openalex.org/S104038378","display_name":"Biochemistry","issn_l":"0006-2960","issn":["0006-2960","1520-4995","1943-295X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biochemistry","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/A5075255077","display_name":"Kiyotaka Shiba","orcid":"https://orcid.org/0000-0001-6459-0204","observed_orcids":["https://orcid.org/0000-0001-6459-0204"]},"institutions":[{"id":"https://openalex.org/I42570316","display_name":"Japanese Foundation For Cancer Research","ror":"https://ror.org/00bv64a69","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I42570316"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kiyotaka Shiba","raw_affiliation_strings":["Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo","institution_ids":["https://openalex.org/I42570316"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017238009","display_name":"Tracy L. Ripmaster","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tracy Ripmaster","raw_affiliation_strings":["Massachusetts Institute of Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066250028","display_name":"Noriko Suzuki","orcid":"https://orcid.org/0000-0001-9130-3944","observed_orcids":["https://orcid.org/0000-0001-9130-3944"]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Noriko Suzuki","raw_affiliation_strings":["Massachusetts Institute of Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113760269","display_name":"R. Nichols","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ralph Nichols","raw_affiliation_strings":["Massachusetts Institute of Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056507445","display_name":"Paul H. Pl\u00f6tz","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Plotz","raw_affiliation_strings":["Massachusetts Institute of Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111517612","display_name":"Tetsuo Noda","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tetsuo Noda","raw_affiliation_strings":["Massachusetts Institute of Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026856074","display_name":"PAUL R. SCHIMMEL","orcid":"https://orcid.org/0000-0002-0448-022X","observed_orcids":["https://orcid.org/0000-0002-0448-022X"]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Schimmel","raw_affiliation_strings":["Massachusetts Institute of Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":1.3626,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.80302816,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"34","issue":"33","first_page":"10340","last_page":"10349"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T11482","display_name":"RNA modifications and cancer","score":0.0,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/alanyl-trna-synthetase","display_name":"alanyl-tRNA synthetase","score":0.9919999837875366},{"id":"https://openalex.org/keywords/human-enzyme","display_name":"human enzyme","score":0.5649999976158142},{"id":"https://openalex.org/keywords/escherichia-coli-enzyme","display_name":"Escherichia coli enzyme","score":0.8759999871253967},{"id":"https://openalex.org/keywords/aminoacylation","display_name":"aminoacylation","score":0.7020000219345093},{"id":"https://openalex.org/keywords/sequence-conservation","display_name":"sequence conservation","score":0.6060000061988831},{"id":"https://openalex.org/keywords/tetramer-formation","display_name":"tetramer formation","score":0.722000002861023},{"id":"https://openalex.org/keywords/monomeric-enzyme","display_name":"monomeric enzyme","score":0.6899999976158142},{"id":"https://openalex.org/keywords/catalytic-core","display_name":"catalytic core","score":0.5609999895095825},{"id":"https://openalex.org/keywords/protein-evolution","display_name":"protein evolution","score":0.3440000116825104}],"concepts":[{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.6610569357872009},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.4441409409046173},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42381638288497925},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4047549068927765},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.37523460388183594},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.362425833940506},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3365703821182251},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.1878301501274109},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.18133142590522766},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.135023295879364},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000412","descriptor_name":"Alanine-tRNA Ligase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000412","descriptor_name":"Alanine-tRNA Ligase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003001","descriptor_name":"Cloning, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018076","descriptor_name":"DNA, Complementary","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/bi00033a004","doi":"https://doi.org/10.1021/bi00033a004","is_oa":false,"landing_page_url":"https://doi.org/10.1021/bi00033a004","pdf_url":null,"source":{"id":"https://openalex.org/S104038378","display_name":"Biochemistry","issn_l":"0006-2960","issn":["0006-2960","1520-4995","1943-295X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biochemistry","raw_type":"journal-article"},{"id":"pmid:7654687","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/7654687","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":"Biochemistry","raw_type":"Comparative Study"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G297911602","display_name":null,"funder_award_id":"GM 15539","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W19869291","https://openalex.org/W1442834576","https://openalex.org/W1510792652","https://openalex.org/W1510824617","https://openalex.org/W1516952587","https://openalex.org/W1548292434","https://openalex.org/W1633739406","https://openalex.org/W1670590392","https://openalex.org/W1814307112","https://openalex.org/W1950941644","https://openalex.org/W1963892922","https://openalex.org/W1969901103","https://openalex.org/W1975404097","https://openalex.org/W1977837589","https://openalex.org/W1978925476","https://openalex.org/W1981529363","https://openalex.org/W1988283573","https://openalex.org/W1991124799","https://openalex.org/W1994056136","https://openalex.org/W2002009265","https://openalex.org/W2016401457","https://openalex.org/W2017980451","https://openalex.org/W2019729932","https://openalex.org/W2021810486","https://openalex.org/W2022592785","https://openalex.org/W2023880708","https://openalex.org/W2027804115","https://openalex.org/W2028528516","https://openalex.org/W2028971512","https://openalex.org/W2030801747","https://openalex.org/W2035391529","https://openalex.org/W2035663056","https://openalex.org/W2039072498","https://openalex.org/W2047789905","https://openalex.org/W2057481603","https://openalex.org/W2057781025","https://openalex.org/W2058414656","https://openalex.org/W2062262417","https://openalex.org/W2063038072","https://openalex.org/W2070592531","https://openalex.org/W2073032519","https://openalex.org/W2074231493","https://openalex.org/W2077588858","https://openalex.org/W2079882489","https://openalex.org/W2081898623","https://openalex.org/W2085791091","https://openalex.org/W2086218516","https://openalex.org/W2086732117","https://openalex.org/W2089269422","https://openalex.org/W2091313066","https://openalex.org/W2093065831","https://openalex.org/W2093109164","https://openalex.org/W2093617423","https://openalex.org/W2139305314","https://openalex.org/W2153012540","https://openalex.org/W2154128645","https://openalex.org/W2165765949"],"related_works":["https://openalex.org/W1814307112","https://openalex.org/W1982678776","https://openalex.org/W2033843196","https://openalex.org/W2078216263","https://openalex.org/W1510824617","https://openalex.org/W1988365324","https://openalex.org/W2021173027","https://openalex.org/W2006372465","https://openalex.org/W2019729932","https://openalex.org/W27707670"],"abstract_inverted_index":{"The":[0,46],"class":[1],"II":[2],"Escherichia":[3],"coli":[4,62,75,103,122,147,179],"and":[5,13,34,77,97,124],"human":[6,43,112,126,149,194],"alanyl-tRNA":[7,44],"synthetases":[8],"cross-acylate":[9],"their":[10],"respective":[11],"tRNAs":[12],"require,":[14],"for":[15,82,110,173,185,227],"aminoacylation,":[16],"an":[17,41,163,224],"acceptor":[18,86,142,218],"helix":[19,219],"G3:U70":[20,220],"base":[21,221],"pair":[22,133,222],"that":[23,118,170,182],"is":[24,171,183],"conserved":[25],"in":[26,36,162],"evolution.":[27],"We":[28],"report":[29],"here":[30],"the":[31,37,52,60,69,73,79,85,101,111,120,125,141,154,157,167,177,192,201,217],"primary":[32],"structure":[33],"expression":[35],"yeast":[38],"Pichia":[39,130],"of":[40,51,72,84,144,156,166,203,211],"active":[42],"synthetase.":[45],"N-terminal":[47],"498":[48],"amino":[49],"acids":[50],"968-residue":[53],"polypeptide":[54],"have":[55],"substantial":[56],"(41%)":[57],"identity":[58],"with":[59,191],"E.":[61,74,102,121,146,178],"protein.":[63,113],"A":[64],"closely":[65],"related":[66],"region":[67,202],"encompasses":[68],"class-defining":[70],"domain":[71,95],"enzyme":[76,123,127,195],"includes":[78],"part":[80],"needed":[81],"recognition":[83],"helix.":[87],"As":[88],"a":[89,108,198,209],"result,":[90],"previously":[91],"reported":[92],"mutagenesis,":[93],"modeling,":[94],"organization,":[96],"biochemical":[98],"characterization":[99],"on":[100,140],"protein":[104],"appear":[105],"valid":[106],"as":[107,197,223],"template":[109],"In":[114,152],"particular,":[115],"we":[116],"show":[117],"both":[119],"purified":[128],"from":[129],"aminoacylate":[131],"9-base":[132],"RNA":[134,225],"duplexes":[135],"whose":[136],"sequences":[137,155],"are":[138],"based":[139],"stems":[143],"either":[145],"or":[148],"alanine":[150],"tRNAs.":[151],"contrast,":[153],"two":[158],"enzymes":[159],"completely":[160],"diverge":[161],"internal":[164],"portion":[165],"C-terminal":[168],"half":[169],"essential":[172],"tetramer":[174],"formation":[175],"by":[176],"enzyme,":[180],"but":[181],"dispensable":[184],"microhelix":[186],"aminoacylation.":[187],"This":[188],"divergence":[189],"correlates":[190],"expressed":[193],"behaving":[196],"monomer.":[199],"Thus,":[200],"close":[204],"sequence":[205],"similarity":[206],"may":[207],"be":[208],"consequence":[210],"strong":[212],"selective":[213],"pressure":[214],"to":[215],"conserve":[216],"signal":[226],"alanine.":[228]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2017,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}