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Structural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis

Enolase, a ubiquitous enzyme, catalyzes the reversible conversion of 2-phospho­glycerate (2PG) to phospho­enolpyruvate (PEP) in the glycolytic pathway of organisms of all three domains of life. The underlying mechanism of the 2PG to PEP conversion has been studied in great detail in previous work, h...

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Autores principales: Ahmad, Mohammed, Jha, Bhavya, Bose, Sucharita, Tiwari, Satish, Dwivedy, Abhisek, Kar, Deepshikha, Pal, Ravikant, Mariadasse, Richard, Parish, Tanya, Jeyakanthan, Jeyaraman, Vinothkumar, Kutti R., Biswal, Bichitra Kumar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10619443/
https://www.ncbi.nlm.nih.gov/pubmed/37860976
http://dx.doi.org/10.1107/S2052252523008485
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author Ahmad, Mohammed
Jha, Bhavya
Bose, Sucharita
Tiwari, Satish
Dwivedy, Abhisek
Kar, Deepshikha
Pal, Ravikant
Mariadasse, Richard
Parish, Tanya
Jeyakanthan, Jeyaraman
Vinothkumar, Kutti R.
Biswal, Bichitra Kumar
author_facet Ahmad, Mohammed
Jha, Bhavya
Bose, Sucharita
Tiwari, Satish
Dwivedy, Abhisek
Kar, Deepshikha
Pal, Ravikant
Mariadasse, Richard
Parish, Tanya
Jeyakanthan, Jeyaraman
Vinothkumar, Kutti R.
Biswal, Bichitra Kumar
author_sort Ahmad, Mohammed
collection PubMed
description Enolase, a ubiquitous enzyme, catalyzes the reversible conversion of 2-phospho­glycerate (2PG) to phospho­enolpyruvate (PEP) in the glycolytic pathway of organisms of all three domains of life. The underlying mechanism of the 2PG to PEP conversion has been studied in great detail in previous work, however that of the reverse reaction remains to be explored. Here we present structural snapshots of Mycobacterium tuberculosis (Mtb) enolase in apo, PEP-bound and two 2PG-bound forms as it catalyzes the conversion of PEP to 2PG. The two 2PG-bound complex structures differed in the conformation of the bound product (2PG) viz the widely reported canonical conformation and a novel binding pose, which we refer to here as the alternate conformation. Notably, we observed two major differences compared with the forward reaction: the presence of Mg(B) is non-obligatory for the reaction and 2PG assumes an alternate conformation that is likely to facilitate its dissociation from the active site. Molecular dynamics studies and binding free energy calculations further substantiate that the alternate conformation of 2PG causes distortions in both metal ion coordination and hydrogen-bonding interactions, resulting in an increased flexibility of the active-site loops and aiding product release. Taken together, this study presents a probable mechanism involved in PEP to 2PG catalysis that is likely to be mediated by the conformational change of 2PG at the active site.
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spelling pubmed-106194432023-11-02 Structural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis Ahmad, Mohammed Jha, Bhavya Bose, Sucharita Tiwari, Satish Dwivedy, Abhisek Kar, Deepshikha Pal, Ravikant Mariadasse, Richard Parish, Tanya Jeyakanthan, Jeyaraman Vinothkumar, Kutti R. Biswal, Bichitra Kumar IUCrJ Research Papers Enolase, a ubiquitous enzyme, catalyzes the reversible conversion of 2-phospho­glycerate (2PG) to phospho­enolpyruvate (PEP) in the glycolytic pathway of organisms of all three domains of life. The underlying mechanism of the 2PG to PEP conversion has been studied in great detail in previous work, however that of the reverse reaction remains to be explored. Here we present structural snapshots of Mycobacterium tuberculosis (Mtb) enolase in apo, PEP-bound and two 2PG-bound forms as it catalyzes the conversion of PEP to 2PG. The two 2PG-bound complex structures differed in the conformation of the bound product (2PG) viz the widely reported canonical conformation and a novel binding pose, which we refer to here as the alternate conformation. Notably, we observed two major differences compared with the forward reaction: the presence of Mg(B) is non-obligatory for the reaction and 2PG assumes an alternate conformation that is likely to facilitate its dissociation from the active site. Molecular dynamics studies and binding free energy calculations further substantiate that the alternate conformation of 2PG causes distortions in both metal ion coordination and hydrogen-bonding interactions, resulting in an increased flexibility of the active-site loops and aiding product release. Taken together, this study presents a probable mechanism involved in PEP to 2PG catalysis that is likely to be mediated by the conformational change of 2PG at the active site. International Union of Crystallography 2023-10-21 /pmc/articles/PMC10619443/ /pubmed/37860976 http://dx.doi.org/10.1107/S2052252523008485 Text en © Mohammed Ahmad et al. 2023 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Research Papers
Ahmad, Mohammed
Jha, Bhavya
Bose, Sucharita
Tiwari, Satish
Dwivedy, Abhisek
Kar, Deepshikha
Pal, Ravikant
Mariadasse, Richard
Parish, Tanya
Jeyakanthan, Jeyaraman
Vinothkumar, Kutti R.
Biswal, Bichitra Kumar
Structural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis
title Structural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis
title_full Structural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis
title_fullStr Structural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis
title_full_unstemmed Structural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis
title_short Structural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis
title_sort structural snapshots of mycobacterium tuberculosis enolase reveal dual mode of 2pg binding and its implication in enzyme catalysis
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10619443/
https://www.ncbi.nlm.nih.gov/pubmed/37860976
http://dx.doi.org/10.1107/S2052252523008485
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