SAM (dependent) I AM: The S-adenosylmethionine-dependent methyltransferase fold

Current Opinion in Structural Biology

Volumn 12, Issue 6, 2002, Pages 783-793

  Martin, Jennifer L ^a   McMillan, Fiona M ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

METHYLTRANSFERASE; S ADENOSYLMETHIONINE;

BINDING SITE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME STRUCTURE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; REVIEW; SEQUENCE ALIGNMENT;

EID: 0036917889     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(02)00391-3     Document Type: Review

References (61)

1. Cheng X., Blumenthal R.M. S-Adenosylmethionine-Dependent Methyltransferases: Structures and Functions. 1999;World Scientific Publishing, Singapore.
2. Vidgren J., Svensson L.A., Liljas A. Crystal structure of catechol O-methyltransferase. Nature. 368:1994;354-358.
3. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242.
4. Cheng X., Kumar S., Posfai J., Pflugrath J.W., Roberts R.J. Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell. 74:1993;299-307.
5. Klimasauskas S., Kumar S., Roberts R.J., Cheng X. HhaI methyltransferase flips its target base out of the DNA helix. Cell. 76:1994;357-369.
6. O'Gara M., Klimasauskas S., Roberts R.J., Cheng X. Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes. J Mol Biol. 261:1996;634-645.
7. O'Gara M., Roberts R.J., Cheng X. A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase. J Mol Biol. 263:1996;597-606.
8. O'Gara M., Horton J.R., Roberts R.J., Cheng X. Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base. Nat Struct Biol. 5:1998;872-877.
9. O'Gara M., Zhang X., Roberts R.J., Cheng X. Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide. J Mol Biol. 287:1999;201-209.
10. Kumar S., Horton J.R., Jones G.D., Walker R.T., Roberts R.J., Cheng X. DNA containing 4′-thio-2′-deoxycytidine inhibits methylation by HhaI methyltransferase. Nucleic Acids Res. 25:1997;2773-2783.
11. Sheikhnejad G., Brank A., Christman J.K., Goddard A., Alvarez E., Ford H. Jr, Marquez V.E., Marasco C.J., Sufrin J.R., O'Gara M., et al. Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine. J Mol Biol. 285:1999;2021-2034.
12. Vilkaitis G., Dong A., Weinhold E., Cheng X., Klimasauskas S. Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J Biol Chem. 275:2000;38722-38730.
13. Reinisch K.M., Chen L., Verdine G.L., Lipscomb W.N. The crystal structure of HaeIII methyltransferase covalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell. 82:1995;143-153.
14. Gong W., O'Gara M., Blumenthal R.M., Cheng X. Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 25:1997;2702-2715.
15. Schluckebier G., Kozak M., Bleimling N., Weinhold E., Saenger W. Differential binding of S-adenosylmethionine S-adenosylhomocysteine and Sinefungin to the adenine-specific DNA methyltransferase M.TaqI. J Mol Biol. 265:1997;56-67.
16. Goedecke K., Pignot M., Goody R.S., Scheidig A.J., Weinhold E. Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nat Struct Biol. 8:2001;121-125.
17. Tran P.H., Korszun Z.R., Cerritelli S., Springhorn S.S., Lacks S.A. Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniae bound to S-adenosylmethionine. Structure. 6:1998;1563-1575.
18. Hodel A.E., Gershon P.D., Shi X., Quiocho F.A. The 1.85 Å structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends. Cell. 85:1996;247-256.
19. Hodel A.E., Gershon P.D., Shi X., Wang S.M., Quiocho F.A. Specific protein recognition of an mRNA cap through its alkylated base. Nat Struct Biol. 4:1997;350-354.
20. Hodel A.E., Gershon P.D., Quiocho F.A. Structural basis for sequence-nonspecific recognition of 5′-capped mRNA by a cap-modifying enzyme. Mol Cell. 1:1998;443-447.
21. Hu G., Gershon P.D., Hodel A.E., Quiocho F.A. mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains. Proc Natl Acad Sci USA. 96:1999;7149-7154.
22. Hu G., Oguro A., Li C., Gershon P.D., Quiocho F.A. The "cap-binding slot" of an mRNA cap-binding protein: quantitative effects of aromatic side chain choice in the double-stacking sandwich with cap. Biochemistry. 41:2002;7677-7687.
23. Yu L., Petros A.M., Schnuchel A., Zhong P., Severin J.M., Walter K., Holzman T.F., Fesik S.W. Solution structure of an rRNA methyltransferase (ErmAM) that confers macrolide-lincosamide-streptogramin antibiotic resistance. Nat Struct Biol. 4:1997;483-489.
24. Bussiere D.E., Muchmore S.W., Dealwis C.G., Schluckebier G., Nienaber V.L., Edalji R.P., Walter K.A., Ladror U.S., Holzman T.F., Abad-Zapatero C. Crystal structure of ErmC′, an rRNA methyltransferase which mediates antibiotic resistance in bacteria. Biochemistry. 37:1998;7103-7112.
25. Schluckebier G., Zhong P., Stewart K.D., Kavanaugh T.J., Abad-Zapatero C. The 2.2 Å structure of the rRNA methyltransferase ErmC′ and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J Mol Biol. 289:1999;277-291.
26. Djordjevic S., Stock A.M. Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine. Structure. 5:1997;545-558.
27. Djordjevic S., Stock A.M. Chemotaxis receptor recognition by protein methyltransferase CheR. Nat Struct Biol. 5:1998;446-450.
28. Fu Z., Hu Y., Konishi K., Takata Y., Ogawa H., Gomi T., Fujioka M., Takusagawa F. Crystal structure of glycine N-methyltransferase from rat liver. Biochemistry. 35:1996;11985-11993.
29. Pattanayek R., Newcomer M.E., Wagner C. Crystal structure of apo-glycine N-methyltransferase (GNMT). Protein Sci. 7:1998;1326-1331.
30. Huang Y., Komoto J., Konishi K., Takata Y., Ogawa H., Gomi T., Fujioka M., Takusagawa F. Mechanisms for auto-inhibition and forced product release in glycine N-methyltransferase: crystal structures of wild-type, mutant R175K and S-adenosylhomocysteine-bound R175K enzymes. J Mol Biol. 298:2000;149-162.
31. Horton J.R., Sawada K., Nishibori M., Zhang X., Cheng X. Two polymorphic forms of human histamine methyltransferase: structural, thermal, and kinetic comparisons. Structure. 9:2001;837-849.
32. Zubieta C., He X.Z., Dixon R.A., Noel J.P. Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases. Nat Struct Biol. 8:2001;271-279.
33. Martin J.L., Begun J., McLeish M.J., Caine J.M., Grunewald G.L. Getting the adrenaline going: crystal structure of the adrenaline-synthesizing enzyme PNMT. Structure. 9:2001;977-985.
34. Komoto J., Huang Y., Takata Y., Yamada T., Konishi K., Ogawa H., Gomi T., Fujioka M., Takusagawa F. Crystal structure of guanidinoacetate methyltransferase from rat liver: a model structure of protein arginine methyltransferase. J Mol Biol. 320:2002;223-235.
35. Huang C.C., Smith C.V., Glickman M.S., Jacobs W.R. Jr, Sacchettini J.C. Crystal structures of mycolic acid cyclopropane synthases from Mycobacterium tuberculosis. J Biol Chem. 277:2002;11559-11569.
36. Zhang X., Zhou L., Cheng X. Crystal structure of the conserved core of protein arginine methyltransferase PRMT3. EMBO J. 19:2000;3509-3519.
37. Weiss V.H., McBride A.E., Soriano M.A., Filman D.J., Silver P.A., Hogle J.M. The structure and oligomerization of the yeast arginine methyltransferase, Hmt1. Nat Struct Biol. 7:2000;1165-1171.
38. Skinner M.M., Puvathingal J.M., Walter R.L., Friedman A.M. Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair. Structure. 8:2000;1189-1201.
39. Griffith S.C., Sawaya M.R., Boutz D.R., Thapar N., Katz J.E., Clarke S., Yeates T.O. Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate. J Mol Biol. 313:2001;1103-1116.
40. Smith C.D., Carson M., Friedman A.M., Skinner M.M., Delucas L., Chantalat L., Weise L., Shirasawa T., Chattopadhyay D. Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-Å resolution and modeling of an isoaspartyl-containing peptide at the active site. Protein Sci. 11:2002;625-635.
41. Ryttersgaard C., Griffith S.C., Sawaya M.R., MacLaren D.C., Clarke S., Yeates T.O. Crystal structure of human L-isoaspartyl methyltransferase. J Biol Chem. 277:2002;10642-10646.
42. Scavetta R.D., Thomas C.B., Walsh M.A., Szegedi S., Joachimiak A., Gumport R.I., Churchill M.E. Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases. Nucleic Acids Res. 28:2000;3950-3961.
43. Wang H., Boisvert D., Kim K.K., Kim R., Kim S.H. Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 Å resolution. EMBO J. 19:2000;317-323.
44. Reinisch K.M., Nibert M.L., Harrison S.C. Structure of the reovirus core at 3.6 Å resolution. Nature. 404:2000;960-967.
45. Egloff M.P., Benarroch D., Selisko B., Romette J.L., Canard B. An RNA cap (nucleoside-2′-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J. 21:2002;2757-2768.
46. Schubot F.D., Chen C.J., Rose J.P., Dailey T.A., Dailey H.A., Wang B.C. Crystal structure of the transcription factor sc-mtTFB offers insights into mitochondrial transcription. Protein Sci. 10:2001;1980-1988.
47. Bugl H., Fauman E.B., Staker B.L., Zheng F., Kushner S.R., Saper M.A., Bardwell J.C., Jakob U. RNA methylation under heat shock control. Mol Cell. 6:2000;349-360. The authors report the structure of a heat shock protein incorporating a SAM-MT fold, showing, for the first time, a link between heat shock and RNA methylation.
48. Dong A., Yoder J.A., Zhang X., Zhou L., Bestor T.H., Cheng X. Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA. Nucleic Acids Res. 29:2001;439-448. This work revealed, for the first time, that a SAM-MT fold does not necessarily impart MT activity to a protein.
49. Korolev S., Ikeguchi Y., Skarina T., Beasley S., Arrowsmith C., Edwards A., Joachimiak A., Pegg A.E., Savchenko A. The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor. Nat Struct Biol. 9:2002;27-31.
50. Lim K., Zhang H., Tempczyk A., Bonander N., Toedt J., Howard A., Eisenstein E., Herzberg O. Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine. Proteins. 45:2001;397-407. One of the first examples from structural genomics showing that the structure of an uncharacterised protein incorporates the SAM-MT fold, thus aiding in assignment of function.
51. Gupta A., Kumar P.H., Dineshkumar T.K., Varshney U., Subramanya H.S. Crystal structure of Rv2118c: an AdoMet-dependent methyltransferase from Mycobacterium tuberculosis H37Rv. J Mol Biol. 312:2001;381-391.
52. Romanowski M.J., Bonanno J.B., Burley S.K. Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold. Proteins. 47:2002;563-567.
53. Cheng X., Roberts R.J. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res. 29:2001;3784-3795.
54. Bujnicki J.M. Homology modelling of the DNA 5mC methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases? Int J Biol Macromol. 27:2000;195-204.
55. Wilson J., Jing C., Walker P., Martin S., Howell S., Blackburn G., Gamblin S., Xiao B. Crystal structure and functional analysis of the histone methyltransferase SET7/9. Cell. 111:2002;105-115.
56. Zhang X., Tamaru H., Khan S., Horton J., Keefe L., Selker E., Cheng X. Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell. 111:2002;117-127.
57. Trievel R., Beach B., Dirk L., Houtz R., Hurley J. Structure and catalytic mechanism of a SET domain protein methyltransferase. Cell. 111:2002;91-103.
58. Jacobs S.A., Harp J.M., Devarakonda S., Kim Y., Rastinejad F., Khorasanizadeh S. The active site of the SET domain is constructed on a knot. Nat Struct Biol. 9:2002;833-838.
59. Min J., Zhang X., Cheng X., Grewal S.I., Xu R.M. Structure of the SET domain histone lysine methyltransferase Clr4. Nat Struct Biol. 9:2002;828-832.
60. Michel G., Sauve V., Larocque R., Li Y., Matte A., Cygler M. The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot. Structure. 10:2002;1303-1315.
61. Nureki O., Shirouzu M., Hashimoto K., Ishitani R., Terada T., Tamakoshi M., Oshima T., Chijimatsu M., Takio K., Vassylyev D.G., et al. An enzyme with a deep trefoil knot for the active-site architecture. Acta Crystallogr D Biol Crystallogr. 58:2002;1129-1137.