Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases

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

Volumn 105, Issue 19, 2008, Pages 6876-6881

  Alian, Akram ^a   Lee, Tom T ^a,c   Griner, Sarah L ^a   Stroud, Robert M ^a,b   Finer Moore, Janet ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Kalypsys Inc   (United States)

Author keywords

RNA modification; Substrate specificity; tRNA; X ray crystallography

Indexed keywords

GLUTAMIC ACID; GLUTAMINE; PROTEIN RUMA; PROTEIN TRMA; RNA; TRANSFER RNA; TRANSFER RNA METHYLTRANSFERASE; BACTERIAL PROTEIN; BACTERIAL RNA; ESCHERICHIA COLI PROTEIN; MUTANT PROTEIN; RUMA PROTEIN, BACTERIA; TRMA PROTEIN, E COLI; TRNA(URACIL 5) METHYLTRANSFERASE; TRNA(URACIL-5)-METHYLTRANSFERASE;

ARTICLE; BASE PAIRING; BINDING SITE; CATALYSIS; CHEMICAL STRUCTURE; CONFORMATION; CONSENSUS SEQUENCE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ESCHERICHIA COLI; HYDROGEN BOND; MUTATION; PRIORITY JOURNAL; PROTEIN RNA BINDING; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BIOLOGICAL MODEL; CHEMISTRY; ENZYMOLOGY; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT;

ESCHERICHIA COLI;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BACTERIAL PROTEINS; CATALYSIS; CONSERVED SEQUENCE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTANT PROTEINS; NUCLEIC ACID CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; RNA, BACTERIAL; RNA, TRANSFER; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY; TRNA METHYLTRANSFERASES;

EID: 44349185734     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0802247105     Document Type: Article

References (25)

1. Agris PF (2004) Decoding the genome: A modified view. Nucleic Acids Res 32:223-238.
2. Moore PB, Steitz TA (2002) The involvement of RNA in ribosome function. Nature 418:229-235.
3. Ofengand J (2002) Ribosomal RNA pseudouridines and pseudouridine synthases. FEBS Lett 514:17-25.
4. 54 methyltransferase. Biochimie 76:1133-1142.
5. 5U1939 methyltransferase from Escherichia coli. J Biol Chem 277:8835-8840.
6. 5U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res 31:4738-4746.
7. Lee TT, Agarwalla S, Stroud RM (2004) Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase. Structure (London) 12:397-407.
8. Lee TT, Agarwalla S, Stroud RM (2005) A unique RNA fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell 120:599-611.
9. Sprinzl M, Vassilenko KS (2005) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 33:D139-D140.
10. 5U54-methyltransferase is not sequence specific. Biochemistry 35:11652-11659.
11. 54-methyltransferase. Biochemistry 30:2999-3002.
12. Montfort WR, et al. (1990) Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an antifolate. Biochemistry 29:6964-6977.
13. Shi H, Moore PB (2000) The crystal structure of yeast phenylalanine tRNA at 1.93-Å resolution: A classic structure revisited. RNA 6:1091-1105.
14. Koshlap KM, Guenther R, Sochacka E, Malkiewicz A, Agris PF (1999) A distinctive RNA fold: The solution structure of an analogue of the yeast tRNAPhe T Psi C domain. Biochemistry 38:8647-8656.
15. Schmitz U, Donati A, James TL, Ulyanov NB, Yao L (1998) Small structural ensembles for a 17-nucleotide mimic of the tRNA T psi C-loop via fitting dipolar relaxation rates with the quadratic programming algorithm. Biopolymers 46:329-342.
16. 54)methyltransferase (TrmA) critical for stability, covalent binding of tRNA, and enzymatic activity. Nucleic Acids Res 35:3297-3305.
17. 54 tRNA methyltransferases. Nucleic Acids Res 28:1374-1380.
18. Du Q, et al. (2002) Internal derivatization of oligonucleotides with selenium for x-ray crystallography using MAD. J Am Chem Soc 124:24-25.
19. Otwinowski Z, Minor W (1997) Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-326.
20. Terwilliger TC, Berendzen J (1999) Automated MAD and MIR structure solution. Acta Crystallogr D 55:849-861.
21. Cowtan K (1994) Joint CCP4 ESF-EACBM Newsl Protein Crystallogr 31:34-38.
22. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D 60:2126-2132.
23. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D 53:240-255.
24. Thompson JD, Higgins DG, Gibson TJ (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.
25. Gouet P, Courcelle E, Stuart DI, Metoz F (1999) ESPript: Analysis of multiple sequence alignments in PostScript. Bioinformatics 15:305-308.