A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Park, Si Hoon | - |
dc.contributor.author | Park, Jaehyun | - |
dc.contributor.author | Lee, Sang Jae | - |
dc.contributor.author | Yang, Woo Seok | - |
dc.contributor.author | Park, Sehan | - |
dc.contributor.author | Kim, Kyungdo | - |
dc.contributor.author | Park, Zee-Yong | - |
dc.contributor.author | Song, Hyun Kyu | - |
dc.date.accessioned | 2021-09-01T00:28:30Z | - |
dc.date.available | 2021-09-01T00:28:30Z | - |
dc.date.created | 2021-06-19 | - |
dc.date.issued | 2019-11-08 | - |
dc.identifier.issn | 2045-2322 | - |
dc.identifier.uri | https://scholar.korea.ac.kr/handle/2021.sw.korea/61914 | - |
dc.description.abstract | The hydroxymethylation of cytosine bases plays a vital role in the phage DNA protection system inside the host Escherichia coli. This modification is known to be catalyzed by the dCMP hydroxymethylase from bacteriophage T4 (T4dCH); structural information on the complexes with the substrate, dCMP and the co-factor, tetrahydrofolate is currently available. However, the detailed mechanism has not been understood clearly owing to a lack of structure in the complex with a reaction intermediate. We have applied the X-ray free electron laser (XFEL) technique to determine a high-resolution structure of a T4dCH D179N active site mutant. The XFEL structure was determined at room temperature and exhibited several unique features in comparison with previously determined structures. Unexpectedly, we observed a bulky electron density at the active site of the mutant that originated from the physiological host (i.e., E. coli). Mass-spectrometric analysis and a cautious interpretation of an electron density map indicated that it was a dTMP molecule. The bound dTMP mimicked the methylene intermediate from dCMP to 5'-hydroxymethy-dCMP, and a critical water molecule for the final hydroxylation was convincingly identified. Therefore, this study provides information that contributes to the understanding of hydroxymethylation. | - |
dc.language | English | - |
dc.language.iso | en | - |
dc.publisher | NATURE PUBLISHING GROUP | - |
dc.subject | SERIAL FEMTOSECOND CRYSTALLOGRAPHY | - |
dc.subject | PROTEIN-STRUCTURE DETERMINATION | - |
dc.subject | HYDRIDE TRANSFER STEP | - |
dc.subject | DEOXYCYTIDYLATE HYDROXYMETHYLASE | - |
dc.subject | THYMIDYLATE SYNTHASE | - |
dc.subject | CRYSTAL-STRUCTURE | - |
dc.subject | BACTERIOPHAGE-T4 | - |
dc.subject | DIFFRACTION | - |
dc.subject | OPERATION | - |
dc.subject | CATALYSIS | - |
dc.title | A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser | - |
dc.type | Article | - |
dc.contributor.affiliatedAuthor | Song, Hyun Kyu | - |
dc.identifier.doi | 10.1038/s41598-019-52825-y | - |
dc.identifier.scopusid | 2-s2.0-85074716104 | - |
dc.identifier.wosid | 000495371200006 | - |
dc.identifier.bibliographicCitation | SCIENTIFIC REPORTS, v.9 | - |
dc.relation.isPartOf | SCIENTIFIC REPORTS | - |
dc.citation.title | SCIENTIFIC REPORTS | - |
dc.citation.volume | 9 | - |
dc.type.rims | ART | - |
dc.type.docType | Article | - |
dc.description.journalClass | 1 | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Science & Technology - Other Topics | - |
dc.relation.journalWebOfScienceCategory | Multidisciplinary Sciences | - |
dc.subject.keywordPlus | SERIAL FEMTOSECOND CRYSTALLOGRAPHY | - |
dc.subject.keywordPlus | PROTEIN-STRUCTURE DETERMINATION | - |
dc.subject.keywordPlus | HYDRIDE TRANSFER STEP | - |
dc.subject.keywordPlus | DEOXYCYTIDYLATE HYDROXYMETHYLASE | - |
dc.subject.keywordPlus | THYMIDYLATE SYNTHASE | - |
dc.subject.keywordPlus | CRYSTAL-STRUCTURE | - |
dc.subject.keywordPlus | BACTERIOPHAGE-T4 | - |
dc.subject.keywordPlus | DIFFRACTION | - |
dc.subject.keywordPlus | OPERATION | - |
dc.subject.keywordPlus | CATALYSIS | - |
Items in ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.
(02841) 서울특별시 성북구 안암로 14502-3290-1114
COPYRIGHT © 2021 Korea University. All Rights Reserved.
Certain data included herein are derived from the © Web of Science of Clarivate Analytics. All rights reserved.
You may not copy or re-distribute this material in whole or in part without the prior written consent of Clarivate Analytics.