The crystal structure of Thermus thermophilus UMP kinase complexed with a phosphoryl group acceptor and donor

Kenji Fukui; Anzu Nishiwaki; Noriko Nakagawa; Seiki Kuramitsu; Ryoji Masui

doi:10.1371/journal.pone.0330398

Peer Review History

Original SubmissionMarch 6, 2025
10 Jun 2025 Decision Letter - Michael Massiah, Editor Dear Dr. Masui, Please submit your revised manuscript by Jul 25 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. 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Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Partly Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: N/A Reviewer #2: N/A ****** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: The manuscript "The crystal structure of Thermus thermophilus UMP kinase complexed with a phosphoryl group acceptor and donor" by Fukui, K et al. describes and compares the crystal structure of ttUMPK to other bacterial and archaeal UMPK structures and reveals a loop movement that contains for the first time a UMPK with both a phosphate group donor and acceptor. Overall, I found the manuscript to be well written with some minor flaws that could be readily fixed but lacks scientific depth which is probably not the authors fault. For example, when comparing movement or sequence it would be nice to have the relevance, ie. is the movement important for activity or stability, does the ligand affinity increase or decrease. These key residues can either be tested or referenced from other structures or manuscripts. Also, sequence based alignment of said residues with other species and the relevance, the authors have included structure based alignment. The structure of ttUMPK is a trimer of dimers, the authors should address whether the interface is conserved and potentially perform mutagenesis to disrupt the interactions which should then be confirmed by SEC and functional assays, this data should then be included in the manuscript. It is worth noting that the authors have included in the manuscript the description of a functional assay for ttUMPK but I only found functional data for Kcat and Km on lines 311-312 of the manuscript with no accompanying figure. Reviewer #2: The present publication describes a ternary complex of tturidine monophosphate kinase (UMPK) with a phosphoryl donor and substrate. Upon comparison with other bacterial UMPK structures, the authors identified conformational changes that occur upon substrate and co-substrate binding. Specifically, a very drastic conformational change is observed at the b5-b6 loop upon ADP-UDP binding, which is also seen upon substrate binding by the amino acid kinases family, to which ttUMPK belongs. This conformational change is not as pronounced in archaeal UMPK. This novel structure serves as a missing piece for proposing a model for conformational changes upon substrate binding in thermophilic UMPKs, thereby expanding the knowledge within this field. I recommend this article for publication with minor revisions: 1. The authors propose that the observed positive electron density at the trimer interface corresponds to GTP, based on previously published structures of UMPKs. However, there is no direct evidence that GTP binds to ttUMPK. Seeing as GTP was not added to the crystallization conditions and that GTP did not have significant effect on UMPK’s enzyme kinetics, one can only speculate on the identity of the observed trimer interface density. Having GTP built into the structure could be misleading. 2. Line 23: “addition, GTP, an allosteric effector, bound to intersubunit cavity in the center of the” This statement seems very definitive, when there is not concrete evidence that GTP is indeed bound to this structure. Binding studies (e.g. ITC) could perhaps address the question of GTP binding. I don’t think binding studies are necessary for publication, but the language should be modified to a more speculatory tone. 3. Line 44: Unclear what is a substrate, analogue, phosphoryl acceptor 4. Oligomeric state of ttUMPK. Have the authors attempted other approaches to determining the oligomeric state of ttUMPK. Techniques like Analytical Ultracentrifugation, Circula Dichroism, and/or SEC-multi angle light scattering are better determinants of oligomeric state than Size Exclusion is. Then again, I do not think this impacts the overall findings from this article. 5. Were all chains containing the substrate and co-substrate compared? I am curious to know if other chains within the AU exhibited similar conformational changes. 6. Label helices and loops in Figure 7 7. Can the activity data be included as a supplement? It might be worth comparing the determined kinetic parameters to those of bacterial UMPK +/- GTP 8. Was the “GTP-free” structure (described in paragraph starting in line 336) treated/prepared differently from the one described published in this study? ****** what does this mean? ). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy Reviewer #1: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0330398.r001
Revision 1
25 Jun 2025 Author Response We found the reviewers’ comments most helpful. We revised the manuscript with considering reviewers' comments as follows. The texts after ==> are our comments on the revision. Review Comments to the Author Reviewer #1: The manuscript "The crystal structure of Thermus thermophilus UMP kinase complexed with a phosphoryl group acceptor and donor" by Fukui, K et al. describes and compares the crystal structure of ttUMPK to other bacterial and archaeal UMPK structures and reveals a loop movement that contains for the first time a UMPK with both a phosphate group donor and acceptor. Overall, I found the manuscript to be well written with some minor flaws that could be readily fixed but lacks scientific depth which is probably not the authors fault. For example, when comparing movement or sequence it would be nice to have the relevance, ie. is the movement important for activity or stability, does the ligand affinity increase or decrease. These key residues can either be tested or referenced from other structures or manuscripts. ==> According to the reviewer's comment, we cited previous studies on mutational analysis of E. coli UMPK (Bucurenci et al., 1997, J. Bacteriol. 180, 473-477) and added the sentence as follows: It was reported that mutation of Arg62, Asp69 and Asp174of E. coli UMPK (ecUMPK), corresponding to Arg55, Asp69 and Asp167 of ttUMPK, resulted in a substantial decrease in activity. We also found a significant decrease in kcat was observed in the Ala- and Glu-substituted mutants of ttUMPK (manuscript in preparation). Also, sequence based alignment of said residues with other species and the relevance, the authors have included structure based alignment. ==> According to the reviewer's comment, we created the sequence logo for the 50 most diverse members of AAK_UMPK-PyrH-Ec (bacterial UMPKs) in the Conserved Domain Database. We think the sequence logo is a better way to examine conservation than sequence alignment. The logo is shown as Figure 6. In addition, we described the method to create sequence logo in the new section "Sequence and structural data analysis" in Materials and Methods as follows: Sequence logos were generated with Weblogo3 for the 50 most diverse members of AAK_UMPK-PyrH-Ec in the Conserved Domain Database (p. 8). The structure of ttUMPK is a trimer of dimers, the authors should address whether the interface is conserved and potentially perform mutagenesis to disrupt the interactions which should then be confirmed by SEC and functional assays, this data should then be included in the manuscript. ==> According to the reviewer's comment, we added the description of the structural details of the subunit interfaces in the new section "Subunit interfaces" (p. 12–13). We made the new figure showing the details of the two interfaces as Figure 7. This revealed that the hydrophobic residues are frequent in the interface. Some of these residues are well conserved, as shown in Figure 6 (the sequence logo). Since many hydrophobic residues are likely to be involved in intersubunit intaraction, it is difficult to predict which residues are critical for oligomerization. It also seems unlikely that site-directed mutation at one or two sites leads to changes in the oligomeric state. Therefore, we have not performed experiments investigating this interaction. It is worth noting that the authors have included in the manuscript the description of a functional assay for ttUMPK but I only found functional data for Kcat and Km on lines 311-312 of the manuscript with no accompanying figure. ==> According to the reviewer's comment, we added a new figure showing the results of enzyme assay of ttUMPK as Figure 10. Reviewer #2: The present publication describes a ternary complex of tturidine monophosphate kinase (UMPK) with a phosphoryl donor and substrate. Upon comparison with other bacterial UMPK structures, the authors identified conformational changes that occur upon substrate and co-substrate binding. Specifically, a very drastic conformational change is observed at the b5-b6 loop upon ADP-UDP binding, which is also seen upon substrate binding by the amino acid kinases family, to which ttUMPK belongs. This conformational change is not as pronounced in archaeal UMPK. This novel structure serves as a missing piece for proposing a model for conformational changes upon substrate binding in thermophilic UMPKs, thereby expanding the knowledge within this field. I recommend this article for publication with minor revisions: 1. The authors propose that the observed positive electron density at the trimer interface corresponds to GTP, based on previously published structures of UMPKs. However, there is no direct evidence that GTP binds to ttUMPK. Seeing as GTP was not added to the crystallization conditions and that GTP did not have significant effect on UMPK’s enzyme kinetics, one can only speculate on the identity of the observed trimer interface density. Having GTP built into the structure could be misleading. ==> According to the reviewer's comment, we deleted a GTP model from Figure 3b (density map) and removed GTP molecules from Figure 2. We also deleted (original) Figures 8 and 9, showing the binding mode of GTP in ttUMPK and its homologues, respectively, and subsequently deleted the texts regarding these figures. After removing GTP from the coordinate file, we performed the refinement again and re-created Figure 3 based on a new electron density map. We also revised the values in Table 1. We have completed the updating of the PDB entry (8YH1) and uploaded the validation reports file upon submitting the revised manuscript. 2. Line 23: “addition, GTP, an allosteric effector, bound to intersubunit cavity in the center of the” This statement seems very definitive, when there is not concrete evidence that GTP is indeed bound to this structure. Binding studies (e.g. ITC) could perhaps address the question of GTP binding. I don’t think binding studies are necessary for publication, but the language should be modified to a more speculatory tone. ==> According to the reviewer's comment, we deleted from Abstract the following sentence: In addition, GTP, an allosteric effector, bound to intersubunit cavity in the center of the hexametric structure. 3. Line 44: Unclear what is a substrate, analogue, phosphoryl acceptor ==> According to the reviewer's comment, we revised the two sentences that are pointed out as follows: In archaea, the crystal structures of UMPK complexed with UMP, UMP-AMPPNP and UTP have been determined for Pyrococcus furiosus [4]. The structures complexed with AMPPNP and UMP-AMPPNP have also been determined for Sulfolobus solfataricus [5]. (p. 3) 4. Oligomeric state of ttUMPK. Have the authors attempted other approaches to determining the oligomeric state of ttUMPK. Techniques like Analytical Ultracentrifugation, Circula Dichroism, and/or SEC-multi angle light scattering are better determinants of oligomeric state than Size Exclusion is. Then again, I do not think this impacts the overall findings from this article. ==> The SEC-MALS and analytical ultracentrifuge are not available to our labs. We employed dynamic light scattering (DLS) to characterize the approximate size of ttUMPK in solution, and the molecular mass was estimated to be 126-135 kDa, assuming a globular shape of the particle. The theoretical molecular mass of the hexameric ttUMPK is 152 kDa. However, this is a preliminary experiment, and we have not perrformed other additional experiments investigating the oligomeric state of ttUMPK. 5. Were all chains containing the substrate and co-substrate compared? I am curious to know if other chains within the AU exhibited similar conformational changes. ==> In the original manuscript, Figure 2c showed the superimposition of the backbones of all chains A–I, and we described as follows: The structure of the nine chains in the asymmetric unit are almost identical (Fig. 2c), but the loops of residues 156-179 (beta5-beta6 loop) show relatively high B-factors (Fig 2d). Following the reviewer's comment, we re-examined the results and found no differences between the chains, describing all nine chains as nearly identical. 6. Label helices and loops in Figure 7 ==> According to the reviewer's comment, we added the labels for helices and strands based on the reference (Ramón-Maiques et al., 2002) and added the sentence to the legend to this figure (renamed to Figure 9): Secondary structure elements are labeled according to the nomenclature of Ramón-Maiques (p. 16). We also revised the phrase from "the loop corresponding to the beta5-beta6 in ttUMPK" to "the loop (beta11-beta14) corresponding to the beta5-beta6 in ttUMPK." (p. 16) 7. Can the activity data be included as a supplement? It might be worth comparing the determined kinetic parameters to those of bacterial UMPK +/- GTP ==> According to the reviewer's comment, we added a new figure showing the results of enzyme assay of ttUMPK as Figure 10. We cited this figure in the text (p. 17). 8. Was the “GTP-free” structure (described in paragraph starting in line 336) treated/prepared differently from the one described published in this study? ==> The diffraction data of the "GTP-free" structure was obtained by using different crystals from those in this study, but the protein solutions were originated from the same preparation. Differences in crystallization conditions may result in differences in the bound ligands. In the process of reviewing the data, we realized that we had made a mistake with the crystallization conditions. Therefore, we revised the description about the crystallization conditions (p. 5). Attachments Attachment Submitted filename: Response To Reviewers.docx https://doi.org/10.1371/journal.pone.0330398.r002
23 Jul 2025 Decision Letter - Michael Massiah, Editor Dear Dr. Masui, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit for PLOS ONE’s publication criteria as it currently stands. While the original reviewers have accepted the revision, there was my comment in the original latter that wanted you to address the previous structure instead of giving the impression of this being the first and only structure. That was not addressed in the revision. Please submit your revised manuscript by Sep 06 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Michael Massiah Academic Editor PLOS ONE Journal Requirements: If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: N/A ****** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: I want to thank the authors' of the manuscript "The crystal structure of Thermus thermophilus UMP kinase complexed with a phosphoryl group acceptor and donor" by Fukui, K. et al. for taking the time and effort to review my comments and address my concerns. I am satisfied with the authors' revised manuscript and recommend it be accepted for publication. Reviewer #2: (No Response) ****** what does this mean? ). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy Reviewer #1: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org https://doi.org/10.1371/journal.pone.0330398.r003
Revision 2
30 Jul 2025 Author Response We found the academic editor's comments most helpful. We revised the manuscript with considering reviewers' comments as follows. The texts after ==> are our comments on the revision. Editor: Furthermore, I realized that I was the academic editor for your recent article on CMP and its complex for which there no mention of in this article. Thus, this article gives the impression that this is the first thermophilic NMPkinase solved with its substrates, which is misleading. It is important to note this upfront and why UMP structure is necessary (sequence comparision etc) and what is learned from your various structure of UMP and substrates vs CMP findings. Please ensure a discussion on the comparison of the two proteins as well. ==> As mentioned in Introduction section, bacterial UMPKs have no sequence similarity to other known NMP kinases, including CMP kinase, but have significant sequence and structural similarity to amino acid kinases. Therefore, in the original version of our manuscript, we did not mention our previous work about T. thermophilus CMPK (Mega et al. 2020). To avoid misleading, we added the following sentence in Introduction: Among T. thermophilus NMP kinases, the crystal structures of CMP kinase in various liganded states have been determined (Mega, 2020). The apo form structure of AMP kinase has also been determined (PDB ID, 3CM0) (p. 4). In addition, to highlight that bacterial UMPK and CMPK belong to different families, we added the following sentence in Results and Discussion: The determined structure confirms that ttUMPK does not resemble CMP kinase and AMP kinase, and shows that its main-chain fold conforms to the amino acid kinase fold (Ramón-Maiques, 2002) (p. 9). As descirbed above, bacterial UMPK and CMPK belong to different protein families. We believe that no useful information can be gained from the (structural) comparison of these two proteins. Therefore, I did not add any further comments about them. Attachments Attachment Submitted filename: Response ToReviewers.docx https://doi.org/10.1371/journal.pone.0330398.r004
1 Aug 2025 Decision Letter - Michael Massiah, Editor The crystal structure of Thermus thermophilus UMP kinase complexed with a phosphoryl group acceptor and donor PONE-D-25-12007R2 Dear Dr. Masui, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support . If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Michael Massiah Academic Editor PLOS ONE Additional Editor Comments (optional): Thanks for addressing my comments in this revision. Reviewers' comments: https://doi.org/10.1371/journal.pone.0330398.r005
Formally Accepted
Acceptance Letter - Michael Massiah, Editor PONE-D-25-12007R2 PLOS ONE Dear Dr. Masui, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Michael Massiah Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0330398.r006

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