Structural determinants and distribution of phosphate specificity in ribonucleotide reductases.
enzyme catalysis
enzyme kinetics
nucleic acid enzymology
nucleoside/nucleotide biosynthesis
nucleoside/nucleotide metabolism
phosphate specificity
ribonucleotide reductases
site-directed mutagenesis
Journal
The Journal of biological chemistry
ISSN: 1083-351X
Titre abrégé: J Biol Chem
Pays: United States
ID NLM: 2985121R
Informations de publication
Date de publication:
08 2021
08 2021
Historique:
received:
09
04
2021
revised:
21
07
2021
accepted:
23
07
2021
pubmed:
28
7
2021
medline:
15
12
2021
entrez:
27
7
2021
Statut:
ppublish
Résumé
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides, the building blocks of DNA. RNRs are specific for either ribonucleoside diphosphates or triphosphates as substrates. As far as is known, oxygen-dependent class I RNRs (NrdAB) all reduce ribonucleoside diphosphates, and oxygen-sensitive class III RNRs (NrdD) are all ribonucleoside triphosphate reducers, whereas the adenosylcobalamin-dependent class II (NrdJ) contains both ribonucleoside diphosphate and triphosphate reducers. However, it is unknown how this specificity is conveyed by the active site of the enzymes and how this feature developed in RNR evolution. By structural comparison of the active sites in different RNRs, we identified the apical loop of the phosphate-binding site as a potential structural determinant of substrate specificity. Grafting two residues from this loop from a diphosphate- to a triphosphate-specific RNR caused a change in preference from ribonucleoside triphosphate to diphosphate substrates in a class II model enzyme, confirming them as the structural determinants of phosphate specificity. The investigation of the phylogenetic distribution of this motif in class II RNRs yielded a likely monophyletic clade with the diphosphate-defining motif. This indicates a single evolutionary-split event early in NrdJ evolution in which diphosphate specificity developed from the earlier triphosphate specificity. For those interesting cases where organisms contain more than one nrdJ gene, we observed a preference for encoding enzymes with diverse phosphate specificities, suggesting that this varying phosphate specificity confers a selective advantage.
Identifiants
pubmed: 34314684
pii: S0021-9258(21)00810-3
doi: 10.1016/j.jbc.2021.101008
pmc: PMC8365446
pii:
doi:
Substances chimiques
Phosphates
0
Ribonucleotide Reductases
EC 1.17.4.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
101008Informations de copyright
Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article.
Références
Nat Biotechnol. 2018 Nov;36(10):996-1004
pubmed: 30148503
Life (Basel). 2015 Feb 27;5(1):604-36
pubmed: 25734234
PLoS Comput Biol. 2008 Feb 29;4(2):e1000002
pubmed: 18463696
Electrophoresis. 2009 Jun;30 Suppl 1:S162-73
pubmed: 19517507
Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4022-7
pubmed: 16537479
Chem Rev. 2003 Jun;103(6):2167-201
pubmed: 12797828
J Biol Chem. 2000 Jun 30;275(26):19449-55
pubmed: 10748010
Nat Biotechnol. 2020 Sep;38(9):1079-1086
pubmed: 32341564
PLoS Comput Biol. 2011 Oct;7(10):e1002195
pubmed: 22039361
Annu Rev Biochem. 2006;75:681-706
pubmed: 16756507
Mol Cell Biochem. 1983;50(1):25-45
pubmed: 6341812
Biochemistry. 2015 Dec 1;54(47):7019-28
pubmed: 26536144
Science. 1999 Mar 5;283(5407):1499-504
pubmed: 10066165
Nat Struct Biol. 2002 Apr;9(4):293-300
pubmed: 11875520
Methods Enzymol. 2001;334:215-27
pubmed: 11398463
ACS Chem Biol. 2010 Oct 15;5(10):933-42
pubmed: 20672854
J Biol Chem. 2017 Nov 17;292(46):19044-19054
pubmed: 28972190
J Biol Chem. 1999 Mar 12;274(11):7182-9
pubmed: 10066778
Proc Natl Acad Sci U S A. 1993 Sep 15;90(18):8352-6
pubmed: 8397403
Mol Oncol. 2016 Nov;10(9):1375-1386
pubmed: 27511871
Bioinformatics. 2014 Oct 15;30(20):2981-2
pubmed: 24996895
Nucleic Acids Res. 2017 Jan 4;45(D1):D313-D319
pubmed: 27899672
Crit Rev Biochem Mol Biol. 2012 Jan-Feb;47(1):50-63
pubmed: 22050358
Nucleic Acids Res. 2018 Jul 2;46(W1):W296-W303
pubmed: 29788355
Curr Protoc Bioinformatics. 2014 Dec 12;48:3.13.1-3.13.16
pubmed: 25501942
Eur J Biochem. 1982 Jun 15;125(1):75-81
pubmed: 7049700
BMC Bioinformatics. 2014 Jan 13;15:7
pubmed: 24410852
PeerJ. 2019 Apr 8;7:e6700
pubmed: 30993041
Front Cell Infect Microbiol. 2014 Apr 28;4:52
pubmed: 24809024
J Bacteriol. 2002 Dec;184(23):6544-50
pubmed: 12426342
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
Nat Struct Mol Biol. 2004 Nov;11(11):1142-9
pubmed: 15475969