Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC

BMC Structural Biology

Steven C Almo¹  Jungwook Kim¹ 

[1] Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA

关键词: Oxidoreductase;    SAM-dependent methyl transferase;    X-ray crystallography;    tRNA modification;   

Others  :  1091417
DOI  :  10.1186/1472-6807-13-5

 received in 2012-12-08, accepted in 2013-04-16,  发布年份 2013

【 摘 要 】

Background

Methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specific recognition of codons ending in A or G. In the biosynthetic pathway responsible for this post-transcriptional modification, the bifunctional enzyme MnmC catalyzes the conversion of its hypermodified substrate carboxymethylaminomethyl uridine (cmnm5U34) to mnm5U34. MnmC catalyzes the flavin adenine dinucleotide (FAD)-dependent oxidative cleavage of carboxymethyl group from cmnm5U34 via an imine intermediate to generate aminomethyl uridine (nm5U34), which is subsequently methylated by S-adenosyl-L-methionine (SAM) to yield methylaminomethyl uridine (mnm5U34).

Results

The X-ray crystal structures of SAM/FAD-bound bifunctional MnmC from Escherichia coli and Yersinia pestis, and FAD-bound bifunctional MnmC from Yersinia pestis were determined and the catalytic functions verified in an in vitro assay.

Conclusion

The crystal structures of MnmC from two Gram negative bacteria reveal the overall architecture of the enzyme and the relative disposition of the two independent catalytic domains: a Rossmann-fold domain containing the SAM binding site and an FAD containing domain structurally homologous to glycine oxidase from Bacillus subtilis. The structures of MnmC also reveal the detailed atomic interactions at the interdomain interface and provide spatial restraints relevant to the overall catalytic mechanism.

【 授权许可】

   
2013 Kim and Almo; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

Figure 8.

Figure 9.

【 参考文献 】

• [1]Juhling F, Morl M, Hartmann RK, Sprinzl M, Stadler PF, Putz J: tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res 2009, 37(Database issue):D159-162.
• [2]Yokoyama SaN S: tRNA: Structure, Biosynthesis, and Function. Edited by Söll D, RajBhandary U. Washington DC: ASM; 1995:207-223.
• [3]Crick FH: Codon–anticodon pairing: the wobble hypothesis. J Mol Biol 1966, 19(2):548-555.
• [4]Agris PF: Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified-wobble hypothesis. Biochimie 1991, 73(11):1345-1349.
• [5]Grosjean H: Fine-tuning of RNA functions by modification and editing. In Berlin. New York: Springer; 2005.
• [6]Nasvall SJ, Chen P, Bjork GR: The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo. RNA 2004, 10(10):1662-1673.
• [7]Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O: Snapshots of tRNA sulphuration via an adenylated intermediate. Nature 2006, 442(7101):419-424.
• [8]Bohme S, Meyer S, Kruger A, Steinhoff HJ, Wittinghofer A, Klare JP: Stabilization of G domain conformations in the tRNA-modifying MnmE-GidA complex observed with double electron electron resonance spectroscopy. J Biol Chem 2010, 285(22):16991-17000.
• [9]Moukadiri I, Prado S, Piera J, Velazquez-Campoy A, Bjork GR, Armengod ME: Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions. Nucleic Acids Res 2009, 37(21):7177-7193.
• [10]Kambampati R, Lauhon CT: MnmA and IscS are required for in vitro 2-thiouridine biosynthesis in Escherichia coli. Biochemistry 2003, 42(4):1109-1117.
• [11]Hagervall TG, Edmonds CG, McCloskey JA, Bjork GR: Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. J Biol Chem 1987, 262(18):8488-8495.
• [12]Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L: Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA 2004, 10(8):1236-1242.
• [13]Pearson D, Carell T: Assay of both activities of the bifunctional tRNA-modifying enzyme MnmC reveals a kinetic basis for selective full modification of cmnm5s2U to mnm5s2U. Nucleic Acids Res 2011, 39(11):4818-4826.
• [14]Kitamura A, Sengoku T, Nishimoto M, Yokoyama S, Bessho Y: Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli. Protein science: a publication of the Protein Society 2011, 20(7):1105-1113.
• [15]Roovers M, Oudjama Y, Kaminska KH, Purta E, Caillet J, Droogmans L, Bujnicki JM: Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA. Proteins 2008, 71(4):2076-2085.
• [16]Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N: ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 2010, 38(Web Server issue):W529-533.
• [17]Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA: PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 2007, 35(Web Server issue):W522-525.
• [18]Holm L, Rosenstrom P: Dali server: conservation mapping in 3D. Nucleic Acids Res 2010, 38(Web Server issue):W545-549.
• [19]Settembre EC, Dorrestein PC, Park JH, Augustine AM, Begley TP, Ealick SE: Structural and mechanistic studies on ThiO, a glycine oxidase essential for thiamin biosynthesis in Bacillus subtilis. Biochemistry 2003, 42(10):2971-2981.
• [20]Dorrestein PC, Zhai H, McLafferty FW, Begley TP: The biosynthesis of the thiazole phosphate moiety of thiamin: the sulfur transfer mediated by the sulfur carrier protein ThiS. Chem Biol 2004, 11(10):1373-1381.
• [21]Job V, Marcone GL, Pilone MS, Pollegioni L: Glycine oxidase from Bacillus subtilis. Characterization of a new flavoprotein. J Biol Chem 2002, 277(9):6985-6993.
• [22]Jamil F, Afza Gardner QT, Bashir Q, Rashid N, Akhtar M: Mechanistic and stereochemical studies of glycine oxidase from Bacillus subtilis strain R5. Biochemistry 2010, 49(34):7377-7383.
• [23]Kitamura A, Nishimoto M, Sengoku T, Shibata R, Jager G, Bjork GR, Grosjean H, Yokoyama S, Bessho Y: Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1). J Biol Chem 2012, 287(52):43950-43960.
• [24]Holden HM, Thoden JB, Raushel FM: Carbamoyl phosphate synthetase: a tunnel runs through it. Curr Opin Struct Biol 1998, 8(6):679-685.
• [25]Dunn MF, Niks D, Ngo H, Barends TR, Schlichting I: Tryptophan synthase: the workings of a channeling nanomachine. Trends Biochem Sci 2008, 33(6):254-264.
• [26]Leys D, Basran J, Scrutton NS: Channelling and formation of ‘active’ formaldehyde in dimethylglycine oxidase. EMBO J 2003, 22(16):4038-4048.
• [27]Srivastava D, Schuermann JP, White TA, Krishnan N, Sanyal N, Hura GL, Tan A, Henzl MT, Becker DF, Tanner JJ: Crystal structure of the bifunctional proline utilization A flavoenzyme from Bradyrhizobium japonicum. Proc Natl Acad Sci USA 2010, 107(7):2878-2883.
• [28]Anderson KS: Fundamental mechanisms of substrate channeling. Methods Enzymol 1999, 308:111-145.
• [29]Minor W, Cymborowski M, Otwinowski Z, Chruszcz M: HKL-3000: the integration of data reduction and structure solution–from diffraction images to an initial model in minutes. Acta Crystallogr D: Biol Crystallogr 2006, 62(Pt 8):859-866.
• [30]McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ: Phaser crystallographic software. J Appl Crystallogr 2007, 40(Pt 4):658-674.
• [31]Emsley P, Cowtan K: Coot: model-building tools for molecular graphics. Acta Crystallogr D: Biol Crystallogr 2004, 60(Pt 12 Pt 1):2126-2132.
• [32]Murshudov GN, Vagin AA, Dodson EJ: Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D: Biol Crystallogr 1997, 53(Pt 3):240-255.
• [33]Lebedev AA, Vagin AA, Murshudov GN: Model preparation in MOLREP and examples of model improvement using X-ray data. Acta Crystallogr D: Biol Crystallogr 2008, 64(Pt 1):33-39.