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Title: Molecular Basis for Autocatalytic Backbone N-Methylation in RiPP Natural Product Biosynthesis

Journal Article · · ACS Chemical Biology

N-methylation of nucleic acids, proteins, and peptides is a chemical modification with significant impact on biological regulation. Despite the simplicity of the structural change, N-methylation can influence diverse functions including epigenetics, protein complex formation, and microtubule stability. While there are limited examples of N-methylation of the α-amino group of bacterial and eukaryotic proteins, there are no examples of catalysts that carry out post-translation methylation of backbone amides in proteins or peptides. Recent studies have identified enzymes that catalyze backbone N-methylation on a peptide substrate, a reaction with little biochemical precedent, in a family of ribosomally synthesized natural products produced in basidiomycetes. Here, we describe the crystal structures of Dendrothele bispora dbOphMA, a methyltransferase that catalyzes multiple N-methylations on the peptide backbone. We further carry out biochemical studies of this catalyst to determine the molecular details that promote this unusual chemical transformation. As a result, the structural and biochemical framework described here could facilitate biotechnological applications of catalysts for the rapid production of backbone N-methylated peptides.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
National Inst. of Health
OSTI ID:
1482230
Journal Information:
ACS Chemical Biology, Vol. 13, Issue 10; ISSN 1554-8929
Publisher:
American Chemical Society (ACS)Copyright Statement
Country of Publication:
United States
Language:
ENGLISH

References (53)

RB1 Methylation by SMYD2 Enhances Cell Cycle Progression through an Increase of RB1 Phosphorylation journal June 2012
Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks journal August 2015
Dolastatin 10, a powerful cytostatic peptide derived from a marine animal journal June 1990
Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB journal October 2014
Structural Biology of Nonribosomal Peptide Synthetases book February 2016
Site-directed, Ligase-Independent Mutagenesis (SLIM): a single-tube methodology approaching 100% efficiency in 4 h journal November 2004
Functional and Structural Characterization of a Cation-dependent O-Methyltransferase from the Cyanobacterium Synechocystis sp. Strain PCC 6803 journal July 2008
Multiple N-Methylation by a Designed Approach Enhances Receptor Selectivity journal November 2007
A Self-Sacrificing N -Methyltransferase Is the Precursor of the Fungal Natural Product Omphalotin journal July 2017
High Specificity in CheR Methyltransferase Function: CheR2 OF PSEUDOMONAS PUTIDA IS ESSENTIAL FOR CHEMOTAXIS, WHEREAS CheR1 IS INVOLVED IN BIOFILM FORMATION journal May 2013
Relationships between chromatin organization and DNA methylation in determining gene expression journal October 1999
Revisiting the enniatins: a review of their isolation, biosynthesis, structure determination and biological activities journal September 2012
Cytotoxic peptides hemiasterlin, hemiasterlin A and hemiasterlin B induce mitotic arrest and abnormal spindle formation journal December 1996
Characterization of the Fast and Promiscuous Macrocyclase from Plant PCY1 Enables the Use of Simple Substrates journal January 2018
N -Methylation of Peptides and Proteins: An Important Element for Modulating Biological Functions journal November 2012
Characterization and structure of DhpI, a phosphonate O -methyltransferase involved in dehydrophos biosynthesis journal September 2010
Protein Arginine Methyltransferases: from Unicellular Eukaryotes to Humans journal June 2007
Variations in DNA Methylation Patterns During the Cell Cycle of HeLa Cells journal January 2007
Mapping and Molecular Modeling ofS-Adenosyl-l-methionine Binding Sites inN-Methyltransferase Domains of the Multifunctional Polypeptide Cyclosporin Synthetase journal January 2003
Autocatalytic backbone N-methylation in a family of ribosomal peptide natural products journal June 2017
A Novel Motif for S -Adenosyl-l-methionine Binding by the Ribosomal RNA Methyltransferase TlyA from Mycobacterium tuberculosis journal December 2016
Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0 journal October 2003
Solid-phase synthesis and characterization of N-methyl-rich peptides: N-methyl-rich peptides journal February 2005
Crystal Structure of a Ternary Complex of DnrK, a Methyltransferase in Daunorubicin Biosynthesis, with Bound Products journal July 2004
XDS journal January 2010
A prevalent peptide-binding domain guides ribosomal natural product biosynthesis journal July 2015
Regulation of chromatin binding by a conformational switch in the tail of the Ran exchange factor RCC1 journal September 2008
The mode of action of the antitumor drug bouvardin, an inhibitor of protein synthesis in eukaryotic cells journal November 1982
The Buccaneer software for automated model building. 1. Tracing protein chains journal August 2006
DNA methylation and DNA methyltransferases journal May 2017
Cyclosporin A and C: New metabolites fromTrichoderma polysporum (Link ex Pers.) Rifai journal January 1976
Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants journal June 2017
Improving Oral Bioavailability of Peptides by Multiple N-Methylation: Somatostatin Analogues journal March 2008
Protein Methyltransferases: A Distinct, Diverse, and Dynamic Family of Enzymes journal December 2015
Omphalotin, A New Cyclic Peptide with Potent Nematicidal Activity from Omphalotus Olearius II. Isolation and Structure Determination journal April 1997
Features and development of Coot journal March 2010
Synthetic routes to NEtXaa4-cyclosporin A derivatives as potential anti-HIV I drugs journal September 2000
REFMAC 5 for the refinement of macromolecular crystal structures journal March 2011
CysG structure reveals tetrapyrrole-binding features and novel regulation of siroheme biosynthesis journal November 2003
Kinetic Landscape of a Peptide Bond-Forming Prolyl Oligopeptidase journal April 2017
Critical roles of non-histone protein lysine methylation in human tumorigenesis journal January 2015
The Molecular Mechanism of Aminopropylation of Peptide-Nucleotide Antibiotic Microcin C journal July 2014
Total Synthesis of Cyclosporine: Access to N-Methylated Peptides via Isonitrile Coupling Reactions journal March 2010
Catalytic promiscuity of a bacterial α- N -methyltransferase journal July 2012
Interactions of the Sponge-Derived Antimitotic Tripeptide Hemiasterlin with Tubulin:  Comparison with Dolastatin 10 and Cryptophycin 1 journal October 1999
Data processing and analysis with the autoPROC toolbox journal March 2011
Experimental phasing with SHELXC / D / E : combining chain tracing with density modification journal March 2010
N-terminal modifications of cellular proteins: The enzymes involved, their substrate specificities and biological effects journal June 2015
S-Adenosylmethionine-Binding Properties of a Bacterial Phospholipid N-Methyltransferase journal May 2011
NRMT is an α-N-methyltransferase that methylates RCC1 and retinoblastoma protein journal August 2010
Regulation of transcription factor activity by interconnected post-translational modifications journal February 2014
The Crystal Structure of the Novobiocin Biosynthetic Enzyme NovP: The First Representative Structure for the TylF O-Methyltransferase Superfamily journal January 2010
Cyclosporin synthetase. The most complex peptide synthesizing multienzyme polypeptide so far described. journal July 1990

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Figures / Tables (7)