Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6.
archaeal-like Holliday junction-resolving enzymes
signature motifs
structure–function relationship
thermophilic bacteriophages
Journal
Acta crystallographica. Section D, Structural biology
ISSN: 2059-7983
Titre abrégé: Acta Crystallogr D Struct Biol
Pays: United States
ID NLM: 101676043
Informations de publication
Date de publication:
01 Feb 2022
01 Feb 2022
Historique:
received:
04
08
2021
accepted:
19
11
2021
entrez:
1
2
2022
pubmed:
2
2
2022
medline:
5
4
2022
Statut:
ppublish
Résumé
This study describes the production, characterization and structure determination of a novel Holliday junction-resolving enzyme. The enzyme, termed Hjc_15-6, is encoded in the genome of phage Tth15-6, which infects Thermus thermophilus. Hjc_15-6 was heterologously produced in Escherichia coli and high yields of soluble and biologically active recombinant enzyme were obtained in both complex and defined media. Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA-Holliday junctions (Hjs). The crystal structure of Hjc_15-6 was determined to 2.5 Å resolution using the selenomethionine single-wavelength anomalous dispersion method. To our knowledge, this is the first crystal structure of an Hj-resolving enzyme originating from a bacteriophage that can be classified as an archaeal type of Hj-resolving enzyme. As such, it represents a new fold for Hj-resolving enzymes from phages. Characterization of the structure of Hjc_15-6 suggests that it may form a dimer, or even a homodimer of dimers, and activity studies show endonuclease activity towards Hjs. Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E-SD-EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages.
Identifiants
pubmed: 35102887
pii: S2059798321012298
doi: 10.1107/S2059798321012298
pmc: PMC8805305
doi:
Substances chimiques
DNA, Cruciform
0
Holliday Junction Resolvases
EC 3.1.21.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
212-227Subventions
Organisme : Horizon 2020 Framework Programme, European Metrology Programme for Innovation and Research
ID : 685778
Informations de copyright
open access.
Références
J Biol Chem. 2016 May 20;291(21):11094-104
pubmed: 27013661
Cold Spring Harb Perspect Biol. 2014 Sep 02;6(9):a023192
pubmed: 25183833
BMC Genomics. 2008 Feb 08;9:75
pubmed: 18261238
Science. 1998 Apr 10;280(5361):279-84
pubmed: 9535656
BMC Bioinformatics. 2005 Jul 12;6:172
pubmed: 16011798
Nat Struct Biol. 2001 Jan;8(1):62-7
pubmed: 11135673
Sci Rep. 2020 Jan 15;10(1):393
pubmed: 31941902
EMBO J. 2004 Aug 4;23(15):2972-81
pubmed: 15257292
J Mol Biol. 2008 Apr 25;378(2):468-80
pubmed: 18355836
Protein Sci. 2020 Jan;29(1):128-140
pubmed: 31606894
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549
pubmed: 29722887
J Basic Microbiol. 2010 Oct;50(5):452-6
pubmed: 20806260
Nature. 2007 Oct 4;449(7162):616-20
pubmed: 17873859
Nucleic Acids Res. 2012 Aug;40(15):7016-45
pubmed: 22638584
J Mol Biol. 2000 Apr 7;297(4):923-32
pubmed: 10736227
Nucleic Acids Res. 2020 Jan 8;48(D1):D265-D268
pubmed: 31777944
Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67
pubmed: 21460454
Biochem Biophys Res Commun. 2008 Dec 5;377(1):89-92
pubmed: 18831965
J Comput Chem. 2004 Oct;25(13):1605-12
pubmed: 15264254
Mol Microbiol. 2013 Sep;89(6):1240-58
pubmed: 23888987
Cell. 1994 Sep 23;78(6):1063-72
pubmed: 7923356
IUCrJ. 2018 Jan 25;5(Pt 2):166-171
pubmed: 29765606
Structure. 2001 Mar 7;9(3):197-204
pubmed: 11286886
Nucleic Acids Res. 2021 Jan 8;49(D1):D344-D354
pubmed: 33156333
Nucleic Acids Res. 2016 Jan 4;44(D1):D7-19
pubmed: 26615191
Microb Ecol. 2001 Aug;42(2):117-125
pubmed: 12024275
J Virol. 1976 Jun;18(3):1000-15
pubmed: 775128
Appl Environ Microbiol. 2009 Jan;75(1):212-23
pubmed: 18997032
Biotechnol Lett. 2005 Jul;27(14):983-90
pubmed: 16132841
Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):8873-8
pubmed: 10430863
Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):386-94
pubmed: 21460457
J Mol Biol. 2006 Dec 8;364(4):667-77
pubmed: 17027029
J Mol Biol. 2007 Sep 21;372(3):774-97
pubmed: 17681537
FEMS Microbiol Lett. 2021 Jun 24;368(12):
pubmed: 34114607
Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9351-3
pubmed: 10944205
Nucleic Acids Res. 2000 Nov 15;28(22):4544-51
pubmed: 11071944
J Virol. 1976 Jun;18(3):992-9
pubmed: 775132
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
pubmed: 20383002
Cell. 1982 Jun;29(2):357-65
pubmed: 6288255
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Sep 1;63(Pt 9):802-6
pubmed: 17768360
Nucleic Acids Res. 2000 Sep 15;28(18):3417-32
pubmed: 10982859
J Virol. 2009 Sep;83(18):9388-97
pubmed: 19587059
Nucleic Acids Res. 2000 Nov 15;28(22):4540-3
pubmed: 11071943
J Biol Chem. 2009 Jan 9;284(2):1190-201
pubmed: 19004818
Bioinformatics. 2009 May 1;25(9):1189-91
pubmed: 19151095
Bacteriophage. 2011 May;1(3):152-164
pubmed: 22164349
Mol Cell Proteomics. 2013 Jan;12(1):14-28
pubmed: 23001859
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32
pubmed: 20124692
Nucleic Acids Res. 2011 Mar;39(4):1187-96
pubmed: 20961958
FEBS Lett. 2017 Apr;591(8):1073-1082
pubmed: 27990631
J Mol Biol. 2001 Jun 22;309(5):1067-76
pubmed: 11399079
Nucleic Acids Res. 2005 Jun 22;33(11):3598-605
pubmed: 15972856
EMBO J. 1999 Mar 15;18(6):1447-58
pubmed: 10075917
Biochemistry. 2001 Jan 16;40(2):387-94
pubmed: 11148032
Nucleic Acids Res. 2014 Jul;42(12):7489-527
pubmed: 24878924
Proteins. 1994 Nov;20(3):279-82
pubmed: 7892176
Nucleic Acids Res. 2001 Sep 15;29(18):3705-27
pubmed: 11557805
Nucleic Acids Res. 2017 Apr 7;45(6):3580-3590
pubmed: 28100693
Arch Virol. 2006 Apr;151(4):663-79
pubmed: 16308675
Proc Natl Acad Sci U S A. 2001 May 8;98(10):5509-14
pubmed: 11331763
Cell Mol Life Sci. 2005 Mar;62(6):685-707
pubmed: 15770420
Biol Direct. 2016 Oct 21;11(1):55
pubmed: 27769290