Analysis of insertions and extensions in the functional evolution of the ribonucleotide reductase family.
allostery
evo-velocity
evolution
structure prediction
Journal
Protein science : a publication of the Protein Society
ISSN: 1469-896X
Titre abrégé: Protein Sci
Pays: United States
ID NLM: 9211750
Informations de publication
Date de publication:
12 2022
12 2022
Historique:
received:
20
09
2022
accepted:
22
10
2022
pubmed:
30
10
2022
medline:
2
12
2022
entrez:
29
10
2022
Statut:
ppublish
Résumé
Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. In this work, we expand on our recent phylogenetic inference of the entire RNR family and describe the evolutionarily relatedness of insertions and extensions around the structurally homologous catalytic barrel. Using evo-velocity and sequence similarity network (SSN) analyses, we show that the N-terminal regulatory motif known as the ATP-cone domain was likely inherited from an ancestral RNR. By combining SSN analysis with AlphaFold2 predictions, we also show that the C-terminal extensions of class II RNRs can contain folded domains that share homology with an Fe-S cluster assembly protein. Finally, using sequence analysis and AlphaFold2, we show that the sequence motif of a catalytically essential insertion known as the finger loop is tightly coupled to the catalytic mechanism. Based on these results, we propose an evolutionary model for the diversification of the RNR family.
Identifiants
pubmed: 36307939
doi: 10.1002/pro.4483
pmc: PMC9669993
doi:
Substances chimiques
Ribonucleotide Reductases
EC 1.17.4.-
Nucleotides
0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e4483Informations de copyright
© 2022 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.
Références
Biochim Biophys Acta. 2015 Aug;1854(8):1019-37
pubmed: 25900361
J Am Chem Soc. 2014 Jun 25;136(25):9001-13
pubmed: 24827372
Cell Syst. 2022 Apr 20;13(4):274-285.e6
pubmed: 35120643
Elife. 2018 Feb 01;7:
pubmed: 29388911
Microbiol Mol Biol Rev. 2008 Mar;72(1):110-25, table of contents
pubmed: 18322036
Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3826-31
pubmed: 12655046
J Biol Chem. 1996 Oct 25;271(43):26582-7
pubmed: 8900130
Biochemistry. 2019 Oct 15;58(41):4169-4182
pubmed: 31553576
Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432
pubmed: 30357350
Annu Rev Biochem. 1988;57:349-74
pubmed: 3052277
Genome Res. 2007 Oct;17(10):1496-504
pubmed: 17785537
Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21046-51
pubmed: 22160671
Mol Syst Biol. 2011 Oct 11;7:539
pubmed: 21988835
Science. 1999 Mar 5;283(5407):1499-504
pubmed: 10066165
Sci Adv. 2022 Apr 29;8(17):eabm2827
pubmed: 35476445
Biochemistry. 1992 Oct 13;31(40):9733-43
pubmed: 1382592
Nat Struct Biol. 2002 Apr;9(4):293-300
pubmed: 11875520
Protein Sci. 2022 Dec;31(12):e4483
pubmed: 36307939
J Mol Biol. 1996 Sep 27;262(3):358-69
pubmed: 8845001
Structure. 2016 Jun 7;24(6):906-17
pubmed: 27133024
Nucleic Acids Res. 2021 Jan 8;49(D1):D344-D354
pubmed: 33156333
Elife. 2016 Jan 12;5:e07141
pubmed: 26754917
J Biol Chem. 2017 Nov 17;292(46):19044-19054
pubmed: 28972190
J Biol Chem. 1999 Mar 12;274(11):7182-9
pubmed: 10066778
Science. 1996 Jan 26;271(5248):477-81
pubmed: 8560260
Biochemistry. 2022 Jan 18;61(2):92-106
pubmed: 34941255
Structure. 2001 Aug;9(8):739-50
pubmed: 11587648
Methods Mol Biol. 2020;2112:29-42
pubmed: 32006276
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Nat Commun. 2019 Jun 14;10(1):2653
pubmed: 31201319
Chem Rev. 2017 Jun 28;117(12):7615-7672
pubmed: 28558231
J Biol Chem. 2006 Sep 1;281(35):25287-96
pubmed: 16829681
PLoS One. 2015 Jul 30;10(7):e0134293
pubmed: 26225432
Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12892-6
pubmed: 7809142
PLoS Comput Biol. 2011 Oct;7(10):e1002195
pubmed: 22039361
Proc Natl Acad Sci U S A. 2018 Oct 2;115(40):10022-10027
pubmed: 30224458
Biochemistry. 2019 Apr 9;58(14):1845-1860
pubmed: 30855138
Cell. 2011 Apr 29;145(3):435-46
pubmed: 21529715
J Biol Chem. 2000 Jun 30;275(26):19443-8
pubmed: 10748029
J Mol Evol. 2002 Aug;55(2):138-52
pubmed: 12107591
Proc Natl Acad Sci U S A. 2018 May 15;115(20):E4594-E4603
pubmed: 29712847
J Mol Microbiol Biotechnol. 2000 Apr;2(2):191-4
pubmed: 10939243
Elife. 2022 Sep 01;11:
pubmed: 36047668
Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):E3756-65
pubmed: 25157154
Nature. 2018 Nov;563(7731):416-420
pubmed: 30429545
Brief Bioinform. 2019 Jul 19;20(4):1160-1166
pubmed: 28968734
J Biol Chem. 2021 Oct;297(4):101137
pubmed: 34461093
Nucleic Acids Res. 2021 Jan 8;49(D1):D480-D489
pubmed: 33237286
Biochemistry. 1994 Oct 25;33(42):12676-85
pubmed: 7918494
PLoS One. 2015 Jul 06;10(7):e0128199
pubmed: 26147435
J Biol Chem. 2000 Dec 1;275(48):38111-9
pubmed: 10984489
J Biol Chem. 2020 Nov 13;295(46):15576-15587
pubmed: 32883811
Curr Top Microbiol Immunol. 2017;407:1-29
pubmed: 28550453
J Biol Chem. 2015 Jul 10;290(28):17339-48
pubmed: 25971975
BMC Genomics. 2009 Dec 08;10:589
pubmed: 19995434
Proc Natl Acad Sci U S A. 1995 Sep 12;92(19):8759-62
pubmed: 7568012
Nat Struct Mol Biol. 2004 Nov;11(11):1142-9
pubmed: 15475969