Catalytic domain of plasmid pAD1 relaxase TraX defines a group of relaxases related to restriction endonucleases

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 33, 2013, Pages 13606-13611

  Francia, María Victoria ^a   Clewell, Don B ^b,c   De La Cruz, Fernando ^d   Moncalián, Gabriel ^d  

^a HOSPITAL UNIVERSITARIO MARQUÉS DE VALDECILLA   (Spain)

^b UNIVERSITY OF MICHIGAN SCHOOL OF DENTISTRY   (United States)

^c UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^d University of Cantabria   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; DNA; PLASMID PAD1 RELAXASE; RESTRICTION ENDONUCLEASE; TRAX PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIUM CONJUGATION; BINDING SITE; CATALYSIS; CONTROLLED STUDY; DNA BINDING; DNA CLEAVAGE; DNA TRANSFER; ENTEROCOCCUS FAECALIS; ENZYME ACTIVE SITE; ENZYME STRUCTURE; GENETICS; IN VIVO STUDY; INVERTED REPEAT; MUTANT; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN MOTIF;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; CATALYTIC DOMAIN; CLONING, MOLECULAR; DNA NUCLEOTIDYLTRANSFERASES; DNA RESTRICTION ENZYMES; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GENETIC COMPLEMENTATION TEST; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS; OLIGONUCLEOTIDES; PLASMIDS; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84882294364     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1310037110     Document Type: Article

References (37)

1. Tomich PK, An FY, Damle SP, Clewell DB (1979) Plasmid-related transmissibility and multiple drug resistance in Streptococcus faecalis subsp. zymogenes strain DS16. Antimicrob Agents Chemother 15(6):828-830.
2. Francia MV, et al. (2001) Completion of the nucleotide sequence of the Enterococcus faecalis conjugative virulence plasmid pAD1 and identification of a second transfer origin. Plasmid 46(2):117-127.
3. Garcillán-Barcia MP, Francia MV, de la Cruz F (2009) The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol Rev 33(3):657-687.
4. Clewell DB, Dunny GM (2002) Conjugation and genetic exchange in enterococci. The Enterococci: Pathogenesis, Molecular Biology and Antibiotic Resistance, ed Gilmore MS (ASM, Washington, DC), pp 265-300.
5. Clewell DB (2007) Properties of Enterococcus faecalis plasmid pAD1, a member of a widely disseminated family of pheromone-responding, conjugative, virulence elements encoding cytolysin. Plasmid 58(3):205-227.
6. Chandler JR, Dunny GM (2004) Enterococcal peptide sex pheromones: Synthesis and control of biological activity. Peptides 25(9):1377-1388.
7. Ehrenfeld EE, Kessler RE, Clewell DB (1986) Identification of pheromone-induced surface proteins in Streptococcus faecalis and evidence of a role for lipoteichoic acid in formation of mating aggregates. J Bacteriol 168(1):6-12.
8. Ehrenfeld EE, Clewell DB (1987) Transfer functions of the Streptococcus faecalis plasmid pAD1: Organization of plasmid DNA encoding response to sex pheromone. J Bacteriol 169(8):3473-3481.
9. Francia MV, Clewell DB (2002) Transfer origins in the conjugative Enterococcus faecalis plasmids pAD1 and pAM373: Identification of the pAD1 nic site, a specific relaxase and a possible TraG-like protein. Mol Microbiol 45(2):375-395.
10. Ike Y, Craig RA, White BA, Yagi Y, Clewell DB (1983) Modification of Streptococcus faecalis sex pheromones after acquisition of plasmid DNA. Proc Natl Acad Sci USA 80(17):5369-5373.
11. Chandler JR, Flynn AR, Bryan EM, Dunny GM (2005) Specific control of endogenous cCF10 pheromone by a conserved domain of the pCF10-encoded regulatory protein PrgY in Enterococcus faecalis. J Bacteriol 187(14):4830-4843.
12. Francia MV, et al. (2004) A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol Rev 28(1):79-100.
13. Zechner EL, et al. (2000) Conjugative-DNA transfer processes. The Horizontal Gene Pool. Bacterial Plasmids and Gene Spread, ed Thomas CM (Harwood, Amsterdam), pp 87-174.
14. Núñez B, De La Cruz F (2001) Two atypical mobilization proteins are involved in plasmid CloDF13 relaxation. Mol Microbiol 39(4):1088-1099.
15. Kelley LA, Sternberg MJ (2009) Protein structure prediction on the Web: A case study using the Phyre server. Nat Protoc 4(3):363-371.
16. Hong M, Fuangthong M, Helmann JD, Brennan RG (2005) Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family. Mol Cell 20(1):131-141.
17. Kumarevel T, et al. (2008) Crystal structure of the MarR family regulatory protein, ST1710, from Sulfolobus tokodaii strain. J Struct Biol 161(1):9-17.
18. Vanamee ES, et al. (2011) Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI. Nucleic Acids Res 39(2):712-719.
19. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K (2012) Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Nucleic Acids Res 40(15):7016-7045.
20. Grandoso G, et al. (2000) Two active-site tyrosyl residues of protein TrwC act sequentially at the origin of transfer during plasmid R388 conjugation. J Mol Biol 295(5):1163-1172.
21. Dostál L, Shao S, Schildbach JF (2011) Tracking F plasmid TraI relaxase processing reactions provides insight into F plasmid transfer. Nucleic Acids Res 39(7):2658-2670.
22. Pansegrau W, Schröder W, Lanka E (1994) Concerted action of three distinct domains in the DNA cleaving-joining reaction catalyzed by relaxase (TraI) of conjugative plasmid RP4. J Biol Chem 269(4):2782-2789.
23. Scherzinger E, Lurz R, Otto S, Dobrinski B (1992) In vitro cleavage of double-and single-stranded DNA by plasmid RSF1010-encoded mobilization proteins. Nucleic Acids Res 20(1):41-48.
24. Guzmán LM, Espinosa M (1997) The mobilization protein, MobM, of the streptococcal plasmid pMV158 specifically cleaves supercoiled DNA at the plasmid oriT. J Mol Biol 266(4):688-702.
25. Zou X, Caufield PW, Li Y, Qi F (2001) Complete nucleotide sequence and characterization of pUA140, a cryptic plasmid from Streptococcus mutans. Plasmid 46(2):77-85.
26. Hickman AB, et al. (2000) Unexpected structural diversity in DNA recombination: The restriction endonuclease connection. Mol Cell 5(6):1025-1034.
27. Moscoso M, del Solar G, Espinosa M (1995) Specific nicking-closing activity of the initiator of replication protein RepB of plasmid pMV158 on supercoiled or singlestranded DNA. J Biol Chem 270(8):3772-3779.
28. Meyer TF, Geider K (1979) Bacteriophage fd gene II-protein. II. Specific cleavage and relaxation of supercoiled RF from filamentous phages. J Biol Chem 254(24): 12642-12646.
29. Asano S, Higashitani A, Horiuchi K (1999) Filamentous phage replication initiator protein gpII forms a covalent complex with the 5? end of the nick it introduced. Nucleic Acids Res 27(8):1882-1889.
30. Moscoso M, Eritja R, Espinosa M (1997) Initiation of replication of plasmid pMV158: Mechanisms of DNA strand-transfer reactions mediated by the initiator RepB protein. J Mol Biol 268(5):840-856.
31. Viadiu H, Aggarwal AK (1998) The role of metals in catalysis by the restriction endonuclease BamHI. Nat Struct Biol 5(10):910-916.
32. Pingoud A, Fuxreiter M, Pingoud V, Wende W (2005) Type II restriction endonucleases: Structure and mechanism. Cell Mol Life Sci 62(6):685-707.
33. Chandler M, et al. (2013) Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat Rev Microbiol 11:525-538.
34. Chen Y, Staddon JH, Dunny GM (2007) Specificity determinants of conjugative DNA processing in the Enterococcus faecalis plasmid pCF10 and the Lactococcus lactis plasmid pRS01. Mol Microbiol 63(5):1549-1564.
35. Pérez-Mendoza D, et al. (2006) The relaxase of the Rhizobium etli symbiotic plasmid shows nic site cis-acting preference. J Bacteriol 188(21):7488-7499.
36. Francia MV, Weaver KE, Goicoechea P, Tille P, Clewell DB (2007) Characterization of an active partition system for the Enterococcus faecalis pheromone-responding plasmid pAD1. J Bacteriol 189(23):8546-8555.
37. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: A sequence logo generator. Genome Res 14(6):1188-1190.