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Items: 33

1.

Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.

Stojković V, Myasnikov AG, Young ID, Frost A, Fraser JS, Fujimori DG.

Nucleic Acids Res. 2020 Jan 28. pii: gkaa037. doi: 10.1093/nar/gkaa037. [Epub ahead of print]

PMID:
31989172
2.

Extended Recognition of the Histone H3 Tail by Histone Demethylase KDM5A.

Petronikolou N, Longbotham JE, Fujimori DG.

Biochemistry. 2020 Feb 11;59(5):647-651. doi: 10.1021/acs.biochem.9b01036. Epub 2020 Jan 30.

PMID:
31985200
3.

cfr(B), cfr(C), and a New cfr-Like Gene, cfr(E), in Clostridium difficile Strains Recovered across Latin America.

Stojković V, Ulate MF, Hidalgo-Villeda F, Aguilar E, Monge-Cascante C, Pizarro-Guajardo M, Tsai K, Tzoc E, Camorlinga M, Paredes-Sabja D, Quesada-Gómez C, Fujimori DG, Rodríguez C.

Antimicrob Agents Chemother. 2019 Dec 20;64(1). pii: e01074-19. doi: 10.1128/AAC.01074-19. Print 2019 Dec 20.

PMID:
31685464
4.

Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling.

Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG.

Nat Commun. 2019 Jan 9;10(1):94. doi: 10.1038/s41467-018-07829-z.

5.

miCLIP-MaPseq, a Substrate Identification Approach for Radical SAM RNA Methylating Enzymes.

Stojković V, Chu T, Therizols G, Weinberg DE, Fujimori DG.

J Am Chem Soc. 2018 Jun 13;140(23):7135-7143. doi: 10.1021/jacs.8b02618. Epub 2018 Jun 5.

PMID:
29782154
6.

Mutations in RNA methylating enzymes in disease.

Stojković V, Fujimori DG.

Curr Opin Chem Biol. 2017 Dec;41:20-27. doi: 10.1016/j.cbpa.2017.10.002. Epub 2017 Oct 20. Review.

7.

Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN.

Fitzsimmons CM, Fujimori DG.

PLoS One. 2016 Nov 30;11(11):e0167298. doi: 10.1371/journal.pone.0167298. eCollection 2016.

8.

Editorial overview: Chemical genetics and epigenetics.

Fujimori DG, Conway SJ.

Curr Opin Chem Biol. 2016 Aug;33:vi-vii. doi: 10.1016/j.cbpa.2016.08.008. No abstract available.

PMID:
27614207
9.

Antibiotic resistance evolved via inactivation of a ribosomal RNA methylating enzyme.

Stojković V, Noda-Garcia L, Tawfik DS, Fujimori DG.

Nucleic Acids Res. 2016 Oct 14;44(18):8897-8907. Epub 2016 Aug 5.

10.

Htm1p-Pdi1p is a folding-sensitive mannosidase that marks N-glycoproteins for ER-associated protein degradation.

Liu YC, Fujimori DG, Weissman JS.

Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):E4015-24. doi: 10.1073/pnas.1608795113. Epub 2016 Jun 28.

11.

Opposing Chromatin Signals Direct and Regulate the Activity of Lysine Demethylase 4C (KDM4C).

Pack LR, Yamamoto KR, Fujimori DG.

J Biol Chem. 2016 Mar 18;291(12):6060-70. doi: 10.1074/jbc.M115.696864. Epub 2016 Jan 8.

12.

Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors.

Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Ortiz Torres I, Oppermann U, Shoichet BK, Fujimori DG.

J Med Chem. 2016 Feb 25;59(4):1580-98. doi: 10.1021/acs.jmedchem.5b01527. Epub 2015 Dec 23.

13.

Functional coupling between writers, erasers and readers of histone and DNA methylation.

Torres IO, Fujimori DG.

Curr Opin Struct Biol. 2015 Dec;35:68-75. doi: 10.1016/j.sbi.2015.09.007. Epub 2015 Nov 9. Review.

14.

Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.

Lu J, Trnka MJ, Roh SH, Robinson PJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S.

J Am Soc Mass Spectrom. 2015 Dec;26(12):2141-51. doi: 10.1007/s13361-015-1235-6. Epub 2015 Sep 1.

15.

Radical SAM-Mediated Methylation of Ribosomal RNA.

Stojković V, Fujimori DG.

Methods Enzymol. 2015;560:355-76. doi: 10.1016/bs.mie.2015.03.002. Epub 2015 Apr 25.

16.

Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism.

Torres IO, Kuchenbecker KM, Nnadi CI, Fletterick RJ, Kelly MJ, Fujimori DG.

Nat Commun. 2015 Feb 17;6:6204. doi: 10.1038/ncomms7204.

17.

Product binding enforces the genomic specificity of a yeast polycomb repressive complex.

Dumesic PA, Homer CM, Moresco JJ, Pack LR, Shanle EK, Coyle SM, Strahl BD, Fujimori DG, Yates JR 3rd, Madhani HD.

Cell. 2015 Jan 15;160(1-2):204-18. doi: 10.1016/j.cell.2014.11.039. Epub 2014 Dec 18.

18.

Radical SAM-mediated methylation reactions.

Fujimori DG.

Curr Opin Chem Biol. 2013 Aug;17(4):597-604. doi: 10.1016/j.cbpa.2013.05.032. Epub 2013 Jul 5. Review.

19.

Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase.

Shiau C, Trnka MJ, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG.

Chem Biol. 2013 Apr 18;20(4):494-9. doi: 10.1016/j.chembiol.2013.03.008.

20.

Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding.

Le DD, Cortesi AT, Myers SA, Burlingame AL, Fujimori DG.

J Am Chem Soc. 2013 Feb 27;135(8):2879-82. doi: 10.1021/ja3108214. Epub 2013 Feb 19.

21.

Covalent intermediate in the catalytic mechanism of the radical S-adenosyl-L-methionine methyl synthase RlmN trapped by mutagenesis.

McCusker KP, Medzihradszky KF, Shiver AL, Nichols RJ, Yan F, Maltby DA, Gross CA, Fujimori DG.

J Am Chem Soc. 2012 Oct 31;134(43):18074-81. doi: 10.1021/ja307855d. Epub 2012 Oct 22.

22.

Protein and nucleic acid methylating enzymes: mechanisms and regulation.

Le DD, Fujimori DG.

Curr Opin Chem Biol. 2012 Dec;16(5-6):507-15. doi: 10.1016/j.cbpa.2012.09.014. Epub 2012 Oct 19. Review.

23.

The chemistry of peptidyltransferase center-targeted antibiotics: enzymatic resistance and approaches to countering resistance.

McCusker KP, Fujimori DG.

ACS Chem Biol. 2012 Jan 20;7(1):64-72. doi: 10.1021/cb200418f. Epub 2011 Dec 30. Review.

24.

RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift.

Yan F, Fujimori DG.

Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):3930-4. doi: 10.1073/pnas.1017781108. Epub 2011 Feb 22.

25.

A novel enzymatic rearrangement.

Fujimori DG.

Chem Biol. 2010 Dec 22;17(12):1269-70. doi: 10.1016/j.chembiol.2010.12.003.

26.

RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA.

Yan F, LaMarre JM, Röhrich R, Wiesner J, Jomaa H, Mankin AS, Fujimori DG.

J Am Chem Soc. 2010 Mar 24;132(11):3953-64. doi: 10.1021/ja910850y.

27.

Hypoxia sensing goes gauche.

Fujimori DG.

Nat Chem Biol. 2009 Apr;5(4):202-3. doi: 10.1038/nchembio0409-202. No abstract available.

PMID:
19295524
28.

Structural analysis of an open active site conformation of nonheme iron halogenase CytC3.

Wong C, Fujimori DG, Walsh CT, Drennan CL.

J Am Chem Soc. 2009 Apr 8;131(13):4872-9. doi: 10.1021/ja8097355.

29.

Halogenation strategies in natural product biosynthesis.

Neumann CS, Fujimori DG, Walsh CT.

Chem Biol. 2008 Feb;15(2):99-109. doi: 10.1016/j.chembiol.2008.01.006. Review.

30.

CD and MCD of CytC3 and taurine dioxygenase: role of the facial triad in alpha-KG-dependent oxygenases.

Neidig ML, Brown CD, Light KM, Fujimori DG, Nolan EM, Price JC, Barr EW, Bollinger JM Jr, Krebs C, Walsh CT, Solomon EI.

J Am Chem Soc. 2007 Nov 21;129(46):14224-31. Epub 2007 Oct 30.

31.

Cloning and characterization of the biosynthetic gene cluster for kutznerides.

Fujimori DG, Hrvatin S, Neumann CS, Strieker M, Marahiel MA, Walsh CT.

Proc Natl Acad Sci U S A. 2007 Oct 16;104(42):16498-503. Epub 2007 Oct 10.

32.

Spectroscopic evidence for a high-spin Br-Fe(IV)-oxo intermediate in the alpha-ketoglutarate-dependent halogenase CytC3 from Streptomyces.

Fujimori DG, Barr EW, Matthews ML, Koch GM, Yonce JR, Walsh CT, Bollinger JM Jr, Krebs C, Riggs-Gelasco PJ.

J Am Chem Soc. 2007 Nov 7;129(44):13408-9. Epub 2007 Oct 16. No abstract available.

PMID:
17939667
33.

What's new in enzymatic halogenations.

Fujimori DG, Walsh CT.

Curr Opin Chem Biol. 2007 Oct;11(5):553-60. Epub 2007 Sep 18. Review.

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