{"created":"2023-05-15T14:58:12.772253+00:00","id":78964,"links":{},"metadata":{"_buckets":{"deposit":"f617c222-fa4a-4682-81c0-fa8da0ebf8a4"},"_deposit":{"created_by":1,"id":"78964","owners":[1],"pid":{"revision_id":0,"type":"depid","value":"78964"},"status":"published"},"_oai":{"id":"oai:repo.qst.go.jp:00078964","sets":["1"]},"author_link":["999300","999302","999299","999303","999301","999304","999305"],"item_8_biblio_info_7":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDate":"2020-02","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"8","bibliographicPageEnd":"4077","bibliographicPageStart":"4071","bibliographicVolumeNumber":"117","bibliographic_titles":[{"bibliographic_title":"Proceedings of the National Academy of Sciences of the United States of America"}]}]},"item_8_description_5":{"attribute_name":"抄録","attribute_value_mlt":[{"subitem_description":"Copper-containing nitrite reductases (CuNIRs) transform nitrite to gaseous nitric oxide,which is a key process in the global nitrogen cycle. The catalytic mechanism has been extensively studied to ultimately achieve rational control of this important geobiochemical reaction. However, accumulated structural biology data show discrepancies with spectroscopic and computational studies; hence, the reaction mechanism is still controversial. In particular, the details of the proton transfer involved in it are largely unknown. This situation arises from\nthe failure of determining positions of hydrogen atoms and protons, which play essential roles at the catalytic site of CuNIRs, even with atomic resolution X-ray crystallography. Here, we determined the 1.50 Å resolution neutron structure of a CuNIR from Geobacillus thermodenitrificans (trimer molecular mass of ∼106 kDa) in its resting state at low pH. Our neutron structure reveals the protonation\nstates of catalytic residues (deprotonated aspartate and protonated histidine), thus providing insights into the catalytic mechanism. We found that a hydroxide ion can exist as a ligand to the catalytic Cu atom in the resting state even at a low pH. This OH-bound Cu site is unexpected from previously given X-ray structures but consistent with a reaction intermediate suggested by computational chemistry. Furthermore, the hydrogen-deuterium exchange ratio in our neutron structure suggests that the intramolecular electron transfer pathway has a hydrogen-bond jump, which is proposed by quantum chemistry. Our study can seamlessly link the structural biology to the computational chemistry of CuNIRs, boosting our understanding of the enzymes at the atomic and electronic levels.","subitem_description_type":"Abstract"}]},"item_8_publisher_8":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"National Academy of Sciences"}]},"item_8_relation_14":{"attribute_name":"DOI","attribute_value_mlt":[{"subitem_relation_type_id":{"subitem_relation_type_id_text":"10.1073/pnas.1918125117","subitem_relation_type_select":"DOI"}}]},"item_8_relation_17":{"attribute_name":"関連サイト","attribute_value_mlt":[{"subitem_relation_type_id":{"subitem_relation_type_id_text":"https://www.pnas.org/content/early/2020/02/07/1918125117","subitem_relation_type_select":"URI"}}]},"item_8_source_id_9":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"0027-8424","subitem_source_identifier_type":"ISSN"}]},"item_access_right":{"attribute_name":"アクセス権","attribute_value_mlt":[{"subitem_access_right":"metadata only access","subitem_access_right_uri":"http://purl.org/coar/access_right/c_14cb"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Fukuda, Yota"}],"nameIdentifiers":[{"nameIdentifier":"999299","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Hirano, Yuu"}],"nameIdentifiers":[{"nameIdentifier":"999300","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Kusaka, Katsuhiro"}],"nameIdentifiers":[{"nameIdentifier":"999301","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Inoue, Tsuyoshi"}],"nameIdentifiers":[{"nameIdentifier":"999302","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Tamada, Taro"}],"nameIdentifiers":[{"nameIdentifier":"999303","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Yuu, Hirano","creatorNameLang":"en"}],"nameIdentifiers":[{"nameIdentifier":"999304","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Taro, Tamada","creatorNameLang":"en"}],"nameIdentifiers":[{"nameIdentifier":"999305","nameIdentifierScheme":"WEKO"}]}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourcetype":"journal article","resourceuri":"http://purl.org/coar/resource_type/c_6501"}]},"item_title":"High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase"}]},"item_type_id":"8","owner":"1","path":["1"],"pubdate":{"attribute_name":"公開日","attribute_value":"2020-02-12"},"publish_date":"2020-02-12","publish_status":"0","recid":"78964","relation_version_is_last":true,"title":["High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase"],"weko_creator_id":"1","weko_shared_id":-1},"updated":"2023-05-15T19:45:32.225603+00:00"}