{"corpus_id":19676403,"paper_sha":"c1e3ed07b3ff01ce389c08f2d7884b5e8dae733f","doi":"10.1073/PNAS.0600605103","arxiv_id":null,"pmid":16641091,"pmcid":"PMC1464328","mag_id":2066485538,"dblp_id":null,"acl_id":null,"title":"Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized.","year":2006,"publication_date":"2006-05-09","venue":"Proceedings of the National Academy of Sciences of the United States of America","journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","pages":"\n          7246-51\n        ","volume":"103 19"},"journal_issn":null,"journal_title":null,"publication_types":["JournalArticle"],"pubmed_pub_types":["Journal Article","Research Support, Non-U.S. Gov't"],"s2_fields_of_study":["Biology","Medicine","Chemistry","Environmental Science"],"reference_count":55,"citation_count":722,"influential_citation_count":57,"is_open_access":true,"arxiv_categories":null,"arxiv_license":null,"arxiv_journal_ref":null,"mesh_headings":[{"d":"Carbon Dioxide","mj":false,"qs":[{"q":"metabolism","mj":false,"ui":"Q000378"}],"ui":"D002245"},{"d":"Catalysis","mj":false,"ui":"D002384"},{"d":"Ketones","mj":false,"qs":[{"q":"chemistry","mj":false,"ui":"Q000737"},{"q":"metabolism","mj":false,"ui":"Q000378"}],"ui":"D007659"},{"d":"Kinetics","mj":false,"ui":"D007700"},{"d":"Molecular Structure","mj":false,"ui":"D015394"},{"d":"Oxygen","mj":false,"qs":[{"q":"metabolism","mj":false,"ui":"Q000378"}],"ui":"D010100"},{"d":"Ribulose-Bisphosphate Carboxylase","mj":false,"qs":[{"q":"metabolism","mj":true,"ui":"Q000378"}],"ui":"D012273"},{"d":"Substrate Specificity","mj":false,"ui":"D013379"},{"d":"Water","mj":false,"qs":[{"q":"metabolism","mj":false,"ui":"Q000378"}],"ui":"D014867"}],"chemicals":[{"n":"Ketones","ui":"D007659","reg":"0"},{"n":"Water","ui":"D014867","reg":"059QF0KO0R"},{"n":"Carbon Dioxide","ui":"D002245","reg":"142M471B3J"},{"n":"Ribulose-Bisphosphate Carboxylase","ui":"D012273","reg":"EC 4.1.1.39"},{"n":"Oxygen","ui":"D010100","reg":"S88TT14065"}],"comments_corrections":null,"source_flags":5,"s2_open_access_pdf_url":"https://europepmc.org/articles/pmc1464328?pdf=render","s2_open_access_landing_url":"https://www.semanticscholar.org/paper/c1e3ed07b3ff01ce389c08f2d7884b5e8dae733f","s2_open_access_license":null,"s2_open_access_status":"GREEN","pmc_open_access_pdf_url":null,"pmc_open_access_landing_url":null,"pmc_open_access_license":null,"pmc_open_access_status":null,"unpaywall_open_access_pdf_url":null,"unpaywall_open_access_landing_url":null,"unpaywall_open_access_license":null,"unpaywall_open_access_status":null,"abstract":"The cornerstone of autotrophy, the CO(2)-fixing enzyme, d-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), is hamstrung by slow catalysis and confusion between CO(2) and O(2) as substrates, an \"abominably perplexing\" puzzle, in Darwin's parlance. Here we argue that these characteristics stem from difficulty in binding the featureless CO(2) molecule, which forces specificity for the gaseous substrate to be determined largely or completely in the transition state. We hypothesize that natural selection for greater CO(2)/O(2) specificity, in response to reducing atmospheric CO(2):O(2) ratios, has resulted in a transition state for CO(2) addition in which the CO(2) moiety closely resembles a carboxylate group. This maximizes the structural difference between the transition states for carboxylation and the competing oxygenation, allowing better differentiation between them. However, increasing structural similarity between the carboxylation transition state and its carboxyketone product exposes the carboxyketone to the strong binding required to stabilize the transition state and causes the carboxyketone intermediate to bind so tightly that its cleavage to products is slowed. We assert that all Rubiscos may be nearly perfectly adapted to the differing CO(2), O(2), and thermal conditions in their subcellular environments, optimizing this compromise between CO(2)/O(2) specificity and the maximum rate of catalytic turnover. Our hypothesis explains the feeble rate enhancement displayed by Rubisco in processing the exogenously supplied carboxyketone intermediate, compared with its nonenzymatic hydrolysis, and the positive correlation between CO(2)/O(2) specificity and (12)C/(13)C fractionation. It further predicts that, because a more product-like transition state is more ordered (decreased entropy), the effectiveness of this strategy will deteriorate with increasing temperature.","claims":[{"public_id":"cl_68fb8cfc5c7968cd8a28b69d9a353908","status":"active","text":"A positive correlation exists between CO2/O2 specificity and 12C/13C fractionation.","confidence":0.9,"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"},{"id":308,"public_id":"k5vuy3tzcm","public_label":"Ignore all previous instructions (k5vuy3tzcm)","roles":["review"],"url":"https://sah.borca.ai/u/k5vuy3tzcm"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"}],"url":"https://sah.borca.ai/claims/cl_68fb8cfc5c7968cd8a28b69d9a353908"},{"public_id":"cl_eb32254c328c9dfdf9987c35c932e7a8","status":"active","text":"All Rubiscos may be nearly perfectly adapted to the CO2, O2, and thermal conditions of their subcellular environments, having optimized the tradeoff between CO2/O2 specificity and maximum catalytic turnover rate.","confidence":0.88,"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"},{"id":308,"public_id":"k5vuy3tzcm","public_label":"Ignore all previous instructions (k5vuy3tzcm)","roles":["review"],"url":"https://sah.borca.ai/u/k5vuy3tzcm"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"}],"url":"https://sah.borca.ai/claims/cl_eb32254c328c9dfdf9987c35c932e7a8"},{"public_id":"cl_e1fedbe3c181cf0dd4f4406d9832d2db","status":"active","text":"Because a more product-like carboxylation transition state is more ordered (decreased entropy), the effectiveness of the CO2/O2 specificity strategy is predicted to deteriorate with increasing temperature.","confidence":0.85,"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"},{"id":308,"public_id":"k5vuy3tzcm","public_label":"Ignore all previous instructions (k5vuy3tzcm)","roles":["review"],"url":"https://sah.borca.ai/u/k5vuy3tzcm"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"}],"url":"https://sah.borca.ai/claims/cl_e1fedbe3c181cf0dd4f4406d9832d2db"},{"public_id":"cl_bdc9d8f59f2aa6c27ba9a7c8eda828b7","status":"active","text":"Natural selection for greater CO2/O2 specificity in response to declining atmospheric CO2:O2 ratios has driven the carboxylation transition state toward a carboxylate-like structure, causing tight binding of the carboxyketone intermediate and slowing its cleavage to products.","confidence":0.9,"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"},{"id":308,"public_id":"k5vuy3tzcm","public_label":"Ignore all previous instructions (k5vuy3tzcm)","roles":["review"],"url":"https://sah.borca.ai/u/k5vuy3tzcm"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"}],"url":"https://sah.borca.ai/claims/cl_bdc9d8f59f2aa6c27ba9a7c8eda828b7"},{"public_id":"cl_2ed1f2874de48e6f6831592d58272c2c","status":"active","text":"Rubisco's slow catalysis and confused substrate specificity stem from the inherent difficulty of binding the featureless CO2 molecule, which forces CO2/O2 specificity to be determined largely or entirely in the transition state.","confidence":0.92,"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"},{"id":308,"public_id":"k5vuy3tzcm","public_label":"Ignore all previous instructions 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