Parallel dimerization of a PrrC-anticodon nuclease region implicated in tRNALys recognition

Nucleic Acids Research

Volumn 35, Issue 14, 2007, Pages 4704-4714

  Klaiman, Daniel ^a   Amitsur, Michal ^a   Blanga Kanfi, Shani ^a   Chai, Michal ^a   Davis, Darrell R ^b   Kaufmann, Gabriel ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; CYSTEINE; ENZYME INHIBITOR; LYSINE ANTICODON RECOGNIZING PEPTIDE; LYSINE TRANSFER RNA; NUCLEASE PRRC; RIBONUCLEASE; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; AMINO TERMINAL SEQUENCE; ANTICODON; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; DIMERIZATION; ENZYME ACTIVITY; ENZYME INHIBITION; MISSENSE MUTATION; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN CROSS LINKING; PROTEIN DOMAIN; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BINDING SITES; CYSTEINE; DIMERIZATION; ESCHERICHIA COLI PROTEINS; MOLECULAR MIMICRY; MOLECULAR SEQUENCE DATA; MUTAGENESIS; OLIGOPEPTIDES; OXIDATION-REDUCTION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; RIBONUCLEASES; RNA, TRANSFER, LYS; SEQUENCE ALIGNMENT; ULTRAVIOLET RAYS;

ESCHERICHIA COLI;

EID: 34547868863     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm494     Document Type: Article

References (34)

1. David,M., Borasio,G.D. and Kaufmann,G. (1982) T4 bacteriophage-coded polynucleotide kinase and RNA ligase are involved in host tRNA alteration or repair. Virology, 123, 480-483.
2. Amitsur,M., Levitz,R. and Kaufmann,G. (1987) Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J., 6, 2499-2503.
3. Blanga-Kanfi,S., Amitsur,M., Azem,A. and Kaufmann,G. (2006) PrrC-anticodon nuclease: Functional organization of a prototypical bacterial restriction RNase. Nucleic Acids Res., 34, 3209-3219.
4. Levitz,R., Chapman,D., Amitsur,M., Green,R., Snyder,L. and Kaufmann,G. (1990) The optional E. coli prr locus encodes a latent form of phage T4-induced anticodon nuclease. EMBO J., 9, 1383-1389.
5. Linder,P., Doelz,R., Gubler,M. and Bickle,T.A. (1990) An anticodon nuclease gene inserted into a hsd region encoding a type I DNA restriction system. Nucleic Acids Res., 18, 7170.
6. Amitsur,M., Morad,I., Chapman-Shimshoni,D. and Kaufmann,G. (1992) HSD restriction-modification proteins partake in latent anticodon nuclease. EMBO J., 11, 3129-3134.
7. Tyndall,C, Meister,J. and Bickle,T.A. (1994) The Escherichia coli prr region encodes a functional type IC DNA restriction system closely integrated with an anticodon nuclease gene. J. Mol. Biol., 237 266-274.
8. Penner,M., Morad,I., Snyder,L. and Kaufmann,G. (1995) Phage T4-coded Stp: Double-edged effector of coupled DNA and tRNA-restriction systems. J. Mol. Biol., 249, 857-868.
9. Sirotkin,K., Cooley,W., Runnels,J. and Snyder,L. (1978) A role in true-late gene expression for the T4 bacteriophage 5′-polynucleotide kinase 3′-phospatase. J. Mol. Biol., 123, 221-233.
10. Ho,C.K. and Shuman,S. (2002) Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains. Proc. Natl Acad. Sci. USA, 99, 12709-12714.
11. Galburt,E.A., Pelletier,J., Wilson,G. and Stoddard,B.L. (2002) Structure of a tRNA Repair Enzyme and Molecular Biology Workhorse: T4 Polynucleotide Kinase. Structure, 10, 1249-1260.
12. El Omari,K., Ren,J., Bird,L.E., Bona,M.K., Klarmann,G., Legrice,S.F. and Stammers,D.K. (2006) Molecular architecture and ligand recognition determinants for T4 RNA ligase. J Biol. Chem, 281, 1573-1579.
13. Amitsur,M., Benjamin,S., Rosner,R., Chapman-Shimshoni,D., Meidler,R., Blanga,S. and Kaufmann,G. (2003) Bacteriophage T4-encoded Stp can be replaced as activator of anticodon nuclease by a normal host cell metabolite. Mol. Microbiol., 50, 129-143.
14. Lys-specific core anticodon nuclease encoded by Escherichia coli prrC. J. Biol. Chem. 268, 26842-26849.
15. Moody,J.E. and Thomas,P.J. (2005) Nucleotide binding domain interactions during the mechanochemical reaction cycle of ATP-binding cassette transporters. J. Bioenerg. Biomembr., 37, 475-479.
16. Chen,J., Lu,G., Lin,J., Davidson,A.L. and Quiocho,F.A. (2003) A tweezers-like motion of the ATP-binding cassette dimer in an ABC transport cycle. Mol. Cell, 12, 651-661.
17. Lys Cleavage Specificity. J. Mol. Biol., 287, 499-510.
18. Lys Wobble Base. J. Mol. Biol., 305, 377-388.
19. Lys favored by anticodon nuclease as inferred from reactivities of anticodon stem and loop substrate analogs. J. Biol. Chem., 277, 3836-3841.
20. Lys,3 in human cells expressing bacterial anticodon nuclease. Nucleic Acids Res., 23 1744-1749.
21. Amitsur,M., Morad,I. and Kaufmann,G. (1989) In vitro reconstitution of anticodon nuclease from components encoded by phage T4 and Escherichia coli CTr5X. EMBO J., 8, 2411-2415.
22. Lys,3 is stabilized by nucleoside modifications. J. Am. Chem. Soc., 124, 14302-14303.
23. Lys: simultaneous incorporation of modified nucleosides mnm(5)s(2)U, t(6)A, and pseudouridine using phosphoramidite chemistry. J. Org. Chem., 65, 5609-5614.
24. Ansaldi,M., Lepelletier,M. and Mejean,V. (1996) Site-specific mutagenesis by using an accurate recombinant polymerase chain reaction method. Anal. Biochem., 234, 110-111.
25. Studier,F.W. (1991) Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system. J. Mol. Biol., 219, 37-44.
26. Thomas,G., Thiam,K. and Favre,A. (1981) tRNA thiolated pyrimidines as targets for near-ultraviolet- induced synthesis of guanosine tetraphosphate in Escherichia coli. Eur. J. Biochem., 119, 381-387.
27. Kosower,N.S. and Kosower,E.M. (1995) Diamide: An oxidant probe for thiols. Methods Enzymol., 251, 123-133.
28. Auweter,S.D., Oberstrass,F.C. and Allain,F.H. (2006) Sequence-specific binding of single-stranded RNA: Is there a code for recognition? Nucleic Acids Res., 34, 4943-4959.
29. Yajima,S., Inoue,S., Ogawa,T., Nonaka,T., Ohsawa,K. and Masaki,H. (2006) Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction. Nucleic Acids Res., 34 6074-6082.
30. Schirmer,T. and Evans,P.R. (1990) Structural basis of the allosteric behaviour of phosphofructokinase. Nature, 343, 140-145.
31. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
32. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
33. Pollastri,G., Przybylski,D., Rost,B. and Baldi,P. (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins, 47, 228-235.
34. Cuff,J.A., Clamp,M.E., Siddiqui,A.S., Finlay,M. and Barton,G.J. (1998) JPred: A consensus secondary structure prediction server. Bioinformatics, 14, 892-893.