Structural analyses of NudT16–ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins

Puchong Thirawatananond, Robert Lyle McPherson, Jasmine Malhi, Sara Nathan, Michael J. Lambrecht, Matthew Brichacek, Paul Hergenrother, Anthony K.L. Leung, Sandra B. Gabelli

Research output: Contribution to journalArticle

Abstract

ADP-ribosylation is a post-translational modification that occurs on chemically diverse amino acids, including aspartate, glutamate, lysine, arginine, serine and cysteine on proteins and is mediated by ADP-ribosyltransferases, including a subset commonly known as poly(ADP-ribose) polymerases. ADP-ribose can be conjugated to proteins singly as a monomer or in polymeric chains as poly(ADP-ribose). While ADP-ribosylation can be reversed by ADP-ribosylhydrolases, this protein modification can also be processed to phosphoribosylation by enzymes possessing phosphodiesterase activity, such as snake venom phosphodiesterase, mammalian ectonucleotide pyrophosphatase/phosphodiesterase 1, Escherichia coli RppH, Legionella pneumophila Sde and Homo sapiens NudT16 (HsNudT16). Our studies here sought to utilize X-ray crystallographic structures of HsNudT16 in complex with monomeric and dimeric ADP-ribose in identifying the active site for binding and processing free and protein-conjugated ADP-ribose into phosphoribose forms. These structural data guide rational design of mutants that widen the active site to better accommodate protein-conjugated ADP-ribose. We identified that several HsNudT16 mutants (Δ17, F36A, and F61S) have reduced activity for free ADP-ribose, similar processing ability against protein-conjugated mono(ADP-ribose), but improved catalytic efficiency for protein-conjugated poly(ADP-ribose). These HsNudT16 variants may, therefore, provide a novel tool to investigate different forms of ADP-ribose.

Original languageEnglish (US)
Article number5940
JournalScientific reports
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2019

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Adenosine Diphosphate Ribose
Ribose
Proteins
Poly Adenosine Diphosphate Ribose
ADP-ribosylarginine hydrolase
arginine glutamate
Adenosine Diphosphate
Catalytic Domain
ADP Ribose Transferases
Legionella pneumophila
Poly(ADP-ribose) Polymerases
Phosphoric Diester Hydrolases
Post Translational Protein Processing
poly(ADP)-ribosylated proteins
Aspartic Acid
Serine
Lysine
Cysteine
X-Rays
Escherichia coli

ASJC Scopus subject areas

  • General

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Thirawatananond, P., McPherson, R. L., Malhi, J., Nathan, S., Lambrecht, M. J., Brichacek, M., ... Gabelli, S. B. (2019). Structural analyses of NudT16–ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins. Scientific reports, 9(1), [5940]. https://doi.org/10.1038/s41598-019-39491-w

Structural analyses of NudT16–ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins. / Thirawatananond, Puchong; McPherson, Robert Lyle; Malhi, Jasmine; Nathan, Sara; Lambrecht, Michael J.; Brichacek, Matthew; Hergenrother, Paul; Leung, Anthony K.L.; Gabelli, Sandra B.

In: Scientific reports, Vol. 9, No. 1, 5940, 01.12.2019.

Research output: Contribution to journalArticle

Thirawatananond, Puchong ; McPherson, Robert Lyle ; Malhi, Jasmine ; Nathan, Sara ; Lambrecht, Michael J. ; Brichacek, Matthew ; Hergenrother, Paul ; Leung, Anthony K.L. ; Gabelli, Sandra B. / Structural analyses of NudT16–ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins. In: Scientific reports. 2019 ; Vol. 9, No. 1.
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