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Title: Enzymatic reconstitution of ribosomal peptide backbone thioamidation

Abstract

Methyl-coenzyme M reductase (MCR) is an essential enzyme found strictly in methanogenic and methanotrophic archaea. MCR catalyzes a reversible reaction involved in the production and consumption of the potent greenhouse gas methane. The α-subunit of this enzyme (McrA) contains several unusual posttranslational modifications, including the only known naturally occurring example of protein thioamidation. We have recently demonstrated by genetic deletion and mass spectrometry that the tfuA and ycaO genes of Methanosarcina acetivorans are involved in thioamidation of Gly465 in the MCR active site. Modification to thioGly has been postulated to stabilize the active site structure of MCR. Herein, we report the in vitro reconstitution of ribosomal peptide thioamidation using heterologously expressed and purified YcaO and TfuA proteins from M. acetivorans. Like other reported YcaO proteins, this reaction is ATP-dependent but requires an external sulfide source. We also reconstitute the thioamidation activity of two TfuA-independent YcaOs from the hyperthermophilic methanogenic archaea Methanopyrus kandleri and Methanocaldococcus jannaschii. Using these proteins, we demonstrate the basis for substrate recognition and regioselectivity of thioamide formation based on extensive mutagenesis, biochemical, and binding studies. Finally, we report nucleotide-free and nucleotide-bound crystal structures for the YcaO proteins from M. kandleri. Sequence and structure-guided mutagenesis with subsequent biochemicalmore » evaluation have allowed us to assign roles for residues involved in thioamidation and confirm that the reaction proceeds via backbone O-phosphorylation. We conclude these data assign a new biochemical reaction to the YcaO superfamily and paves the way for further characterization of additional peptide backbone posttranslational modifications.« less

Authors:
 [1];  [1]; ORCiD logo [1];  [1]; ORCiD logo [1]
  1. Univ. of Illinois at Urbana-Champaign, IL (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1499738
Grant/Contract Number:  
GM097142
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 115; Journal Issue: 12; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; thioamide; methanogen; posttranslational modification; YcaO; methyl-coenzyme M reductase

Citation Formats

Mahanta, Nilkamal, Liu, Andi, Dong, Shihui, Nair, Satish K., and Mitchell, Douglas A. Enzymatic reconstitution of ribosomal peptide backbone thioamidation. United States: N. p., 2018. Web. doi:10.1073/pnas.1722324115.
Mahanta, Nilkamal, Liu, Andi, Dong, Shihui, Nair, Satish K., & Mitchell, Douglas A. Enzymatic reconstitution of ribosomal peptide backbone thioamidation. United States. doi:10.1073/pnas.1722324115.
Mahanta, Nilkamal, Liu, Andi, Dong, Shihui, Nair, Satish K., and Mitchell, Douglas A. Mon . "Enzymatic reconstitution of ribosomal peptide backbone thioamidation". United States. doi:10.1073/pnas.1722324115. https://www.osti.gov/servlets/purl/1499738.
@article{osti_1499738,
title = {Enzymatic reconstitution of ribosomal peptide backbone thioamidation},
author = {Mahanta, Nilkamal and Liu, Andi and Dong, Shihui and Nair, Satish K. and Mitchell, Douglas A.},
abstractNote = {Methyl-coenzyme M reductase (MCR) is an essential enzyme found strictly in methanogenic and methanotrophic archaea. MCR catalyzes a reversible reaction involved in the production and consumption of the potent greenhouse gas methane. The α-subunit of this enzyme (McrA) contains several unusual posttranslational modifications, including the only known naturally occurring example of protein thioamidation. We have recently demonstrated by genetic deletion and mass spectrometry that the tfuA and ycaO genes of Methanosarcina acetivorans are involved in thioamidation of Gly465 in the MCR active site. Modification to thioGly has been postulated to stabilize the active site structure of MCR. Herein, we report the in vitro reconstitution of ribosomal peptide thioamidation using heterologously expressed and purified YcaO and TfuA proteins from M. acetivorans. Like other reported YcaO proteins, this reaction is ATP-dependent but requires an external sulfide source. We also reconstitute the thioamidation activity of two TfuA-independent YcaOs from the hyperthermophilic methanogenic archaea Methanopyrus kandleri and Methanocaldococcus jannaschii. Using these proteins, we demonstrate the basis for substrate recognition and regioselectivity of thioamide formation based on extensive mutagenesis, biochemical, and binding studies. Finally, we report nucleotide-free and nucleotide-bound crystal structures for the YcaO proteins from M. kandleri. Sequence and structure-guided mutagenesis with subsequent biochemical evaluation have allowed us to assign roles for residues involved in thioamidation and confirm that the reaction proceeds via backbone O-phosphorylation. We conclude these data assign a new biochemical reaction to the YcaO superfamily and paves the way for further characterization of additional peptide backbone posttranslational modifications.},
doi = {10.1073/pnas.1722324115},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
issn = {0027-8424},
number = 12,
volume = 115,
place = {United States},
year = {2018},
month = {3}
}

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    Works referencing / citing this record:

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    journal, September 2018

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