Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA methyltransferase, in complex with S-adenosyl-L-methionine

Protein Science

Volumn 19, Issue 3, 2010, Pages 617-624

  Ta, Hai Minh ^a   Kim, Kyeong Kyu ^a  

^a Sungkyunkwan University School of Medicine   (South Korea)

Author keywords

Crystal; Methyltransferase; S adenosyl L methionine; Sp1610; tRNA

Indexed keywords

BACTERIAL PROTEIN; PROTEIN SP 1610; S ADENOSYLMETHIONINE; TRANSFER RNA METHYLTRANSFERASE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; METHYLATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; STREPTOCOCCUS PNEUMONIAE; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BINDING SITES; CATALYSIS; CRYSTALLOGRAPHY, X-RAY; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; S-ADENOSYLMETHIONINE; SEQUENCE ALIGNMENT; STATIC ELECTRICITY; STREPTOCOCCUS PNEUMONIAE; TRNA METHYLTRANSFERASES;

BACTERIA (MICROORGANISMS); STREPTOCOCCUS PNEUMONIAE;

EID: 77249106059     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.319     Document Type: Article

References (25)

1. Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM (2006) MODOMICS: a database of RNA modification pathways. Nucleic Acids Res 34:D145-D149.
2. Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 26:148-153.
3. Mart?́nez Giménez JA, Sáez GT, Seisdedos RT (1998) On the function of modified nucleosides in the RNA-world. J Theor Biol 194:485-490.
4. Vermeulen A, McCallum SA, Pardi A (2005) Comparison of the global structure and dynamics of native and unmodified tRNAval. Biochemistry 44:6024-6033.
5. Nakanishi K, Nureki O (2006) Recent progress of structural biology of tRNA processing and modification. Mol Cells 19:157-166.
6. Schubert HL, Blumenthal RM, Cheng X (2003) Many paths to methyltransfer: a chronicle of convergence. Trends Biochem Sci 28:329-335.
7. Kozbial PZ, Mushegian AR (2005) Natural history of S-adenosylmethionine- binding proteins. BMC Struct Biol 14:5-19.
8. Martin JL, Fiona M McMillan FM (2002) SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold. Curr Opin Struct Biol 12:783-793.
9. Constantine KL, Krystek SR, Healy MD, Doyle ML, Siemers NO, Thanassi J, Yan N, Xie D, Goldfarb V, Yanchunas J, Tao L, Dougherty BA, Farmer BT, II (2005) Structural and functional characterization of CFE88: evidence that a conserved and essential bacterial protein is a methyltransferase. Protein Sci 14:1472-1484.
10. 1A22 methyltransferase (TrmK). Nucleic Acids Res 36:3252-3262.
11. Thanassi JA, Hartman-Neumann SL, Dougherty TJ, Dougherty BA, Pucci MJ (2002) Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res 30:3152-3162.
12. Thompson JD, Higgins DG, and 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.
13. Gouet P, Robert X, Courcelle E (2003) ESPript/END-script: extracting and redering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31:3320-3323.
14. Holm L, Sander C (1998) Touring protein fold space with Dali/FSSP. Nucleic Acids Res 26:316-319.
15. Bheemanaik S, Reddy YV, Rao DN (2006) Structure, function and mechanism of exocyclic DNA methyltransferases. Biochem J 399:177-190.
16. Goto-Ito S, Ito T, Kuratani M, Bessho Y, Yokoyama S (2009) Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Nat Struct Mol Biol 16:1109-1115.
17. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-326.
18. Terwilliger TC, Berendzen J (1999) Automated MAD and MIR structure solution. Acta Crystallogr Sect D 55:849-861.
19. Terwilliger TC (2003) Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr Sect D 59:38-44.
20. Morris RJ, Perrakis A, Lamzin VS (2003) ARP/wARP and automatic interpretation of protein electron density maps. Methods Enzymol 374:229-244.
21. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr Sect D 60: 2126-2132.
22. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr Sect D 53:240-255.
23. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereo-chemical quality of protein structures. J Appl Crystallogr 26:283-291.
24. Vagin A, Teplyakov A (2000) An approach to multi-copy search in molecular replacement. Acta Cryst D 56: 1622-1624.
25. DeLanoWL(2002)ThePyMOLmolecular graphics system on world wide web.Available at: http://www.pymol.org.