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Insertions and deletions mediated functional divergence of Rossmann fold enzymes

Nucleobase-containing coenzymes are hypothesized to be relics of an early RNA-based world that preceded the emergence of proteins. Despite the importance of coenzyme–protein synergisms, their emergence and evolution remain understudied. An excellent target to address this issue is the Rossmann fold,...

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Autores principales: Toledo-Patiño, Saacnicteh, Pascarelli, Stefano, Uechi, Gen-ichiro, Laurino, Paola
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9860332/
https://www.ncbi.nlm.nih.gov/pubmed/36417431
http://dx.doi.org/10.1073/pnas.2207965119
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author Toledo-Patiño, Saacnicteh
Pascarelli, Stefano
Uechi, Gen-ichiro
Laurino, Paola
author_facet Toledo-Patiño, Saacnicteh
Pascarelli, Stefano
Uechi, Gen-ichiro
Laurino, Paola
author_sort Toledo-Patiño, Saacnicteh
collection PubMed
description Nucleobase-containing coenzymes are hypothesized to be relics of an early RNA-based world that preceded the emergence of proteins. Despite the importance of coenzyme–protein synergisms, their emergence and evolution remain understudied. An excellent target to address this issue is the Rossmann fold, the most catalytically diverse and abundant protein architecture in nature. We investigated two main Rossmann lineages: the nicotinamide adenine dinucleotide phosphate (NAD(P)) and the S-adenosyl methionine (SAM)- binding superfamilies. To identify the evolutionary changes that lead to a coenzyme specificity switch on these superfamilies, we performed structural and sequence-based Hidden Markov model analysis to systematically search for key motifs in their coenzyme-binding pockets. Our analyses revealed that through insertions and deletions (InDels) and a residue substitution, the ancient β1−loop−α1 coenzyme-binding structure of NAD(P) could be reshaped into the SAM-binding β1−loop−α1 structure. To experimentally prove this obsevation, we removed three amino acids from the NAD(P)-binding pocket and solved the structure of the resulting mutant, revealing the characteristic loop features of the SAM-binding pocket. To confirm the binding to SAM, we performed isothermal titration calorimetry measurements. Molecular dynamics simulations also corroborated the role of InDels in abolishing NAD binding and acquiring SAM binding. Our results uncovered how nature may have utilized insertions and deletions to optimize the different coenzyme-binding pockets and the distinct functionalities observed for Rossmann superfamilies. This work also proposes a general mechanism by which protein templates could have been recycled through the course of evolution to adopt different coenzymes and confer distinct chemistries.
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spelling pubmed-98603322023-05-23 Insertions and deletions mediated functional divergence of Rossmann fold enzymes Toledo-Patiño, Saacnicteh Pascarelli, Stefano Uechi, Gen-ichiro Laurino, Paola Proc Natl Acad Sci U S A Biological Sciences Nucleobase-containing coenzymes are hypothesized to be relics of an early RNA-based world that preceded the emergence of proteins. Despite the importance of coenzyme–protein synergisms, their emergence and evolution remain understudied. An excellent target to address this issue is the Rossmann fold, the most catalytically diverse and abundant protein architecture in nature. We investigated two main Rossmann lineages: the nicotinamide adenine dinucleotide phosphate (NAD(P)) and the S-adenosyl methionine (SAM)- binding superfamilies. To identify the evolutionary changes that lead to a coenzyme specificity switch on these superfamilies, we performed structural and sequence-based Hidden Markov model analysis to systematically search for key motifs in their coenzyme-binding pockets. Our analyses revealed that through insertions and deletions (InDels) and a residue substitution, the ancient β1−loop−α1 coenzyme-binding structure of NAD(P) could be reshaped into the SAM-binding β1−loop−α1 structure. To experimentally prove this obsevation, we removed three amino acids from the NAD(P)-binding pocket and solved the structure of the resulting mutant, revealing the characteristic loop features of the SAM-binding pocket. To confirm the binding to SAM, we performed isothermal titration calorimetry measurements. Molecular dynamics simulations also corroborated the role of InDels in abolishing NAD binding and acquiring SAM binding. Our results uncovered how nature may have utilized insertions and deletions to optimize the different coenzyme-binding pockets and the distinct functionalities observed for Rossmann superfamilies. This work also proposes a general mechanism by which protein templates could have been recycled through the course of evolution to adopt different coenzymes and confer distinct chemistries. National Academy of Sciences 2022-11-23 2022-11-29 /pmc/articles/PMC9860332/ /pubmed/36417431 http://dx.doi.org/10.1073/pnas.2207965119 Text en Copyright © 2022 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Biological Sciences
Toledo-Patiño, Saacnicteh
Pascarelli, Stefano
Uechi, Gen-ichiro
Laurino, Paola
Insertions and deletions mediated functional divergence of Rossmann fold enzymes
title Insertions and deletions mediated functional divergence of Rossmann fold enzymes
title_full Insertions and deletions mediated functional divergence of Rossmann fold enzymes
title_fullStr Insertions and deletions mediated functional divergence of Rossmann fold enzymes
title_full_unstemmed Insertions and deletions mediated functional divergence of Rossmann fold enzymes
title_short Insertions and deletions mediated functional divergence of Rossmann fold enzymes
title_sort insertions and deletions mediated functional divergence of rossmann fold enzymes
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9860332/
https://www.ncbi.nlm.nih.gov/pubmed/36417431
http://dx.doi.org/10.1073/pnas.2207965119
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