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Evolution of the bacterial nucleosidase PpnN and its relation to the stringent response.

Bærentsen RL, Brodersen DE, Zhang YE.

Microb Cell. 2019 Jul 16;6(9):450-453. doi: 10.15698/mic2019.09.692.


The E. coli HicB Antitoxin Contains a Structurally Stable Helix-Turn-Helix DNA Binding Domain.

Manav MC, Turnbull KJ, Jurėnas D, Garcia-Pino A, Gerdes K, Brodersen DE.

Structure. 2019 Nov 5;27(11):1675-1685.e3. doi: 10.1016/j.str.2019.08.008. Epub 2019 Sep 5.


Serine-Threonine Kinases Encoded by Split hipA Homologs Inhibit Tryptophanyl-tRNA Synthetase.

Vang Nielsen S, Turnbull KJ, Roghanian M, Bærentsen R, Semanjski M, Brodersen DE, Macek B, Gerdes K.

mBio. 2019 Jun 18;10(3). pii: e01138-19. doi: 10.1128/mBio.01138-19.


(p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch.

Zhang YE, Bærentsen RL, Fuhrer T, Sauer U, Gerdes K, Brodersen DE.

Mol Cell. 2019 Jun 20;74(6):1239-1249.e4. doi: 10.1016/j.molcel.2019.03.035. Epub 2019 Apr 22.


The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism.

Hove-Jensen B, Brodersen DE, Manav MC.

Microbiol Mol Biol Rev. 2018 Dec 19;83(1). pii: e00040-18. doi: 10.1128/MMBR.00040-18. Print 2019 Mar. Review.


The RES domain toxins of RES-Xre toxin-antitoxin modules induce cell stasis by degrading NAD+

Skjerning RB, Senissar M, Winther KS, Gerdes K, Brodersen DE.

Mol Microbiol. 2019 Jan;111(1):221-236. doi: 10.1111/mmi.14150. Epub 2018 Nov 11.


The Abc of Phosphonate Breakdown: A Mechanism for Bacterial Survival.

Manav MC, Sofos N, Hove-Jensen B, Brodersen DE.

Bioessays. 2018 Nov;40(11):e1800091. doi: 10.1002/bies.201800091. Epub 2018 Sep 9. Review.


Publisher Correction: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity.

He F, Bhoobalan-Chitty Y, Van LB, Kjeldsen AL, Dedola M, Makarova KS, Koonin EV, Brodersen DE, Peng X.

Nat Microbiol. 2018 Sep;3(9):1076. doi: 10.1038/s41564-018-0184-9.


Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity.

He F, Bhoobalan-Chitty Y, Van LB, Kjeldsen AL, Dedola M, Makarova KS, Koonin EV, Brodersen DE, Peng X.

Nat Microbiol. 2018 Apr;3(4):461-469. doi: 10.1038/s41564-018-0120-z. Epub 2018 Mar 5. Erratum in: Nat Microbiol. 2018 Sep;3(9):1076.


Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology.

Harms A, Brodersen DE, Mitarai N, Gerdes K.

Mol Cell. 2018 Jun 7;70(5):768-784. doi: 10.1016/j.molcel.2018.01.003. Epub 2018 Feb 3. Review.


Structural basis for (p)ppGpp synthesis by the Staphylococcus aureus small alarmone synthetase RelP.

Manav MC, Beljantseva J, Bojer MS, Tenson T, Ingmer H, Hauryliuk V, Brodersen DE.

J Biol Chem. 2018 Mar 2;293(9):3254-3264. doi: 10.1074/jbc.RA117.001374. Epub 2018 Jan 11.


Structural conservation of the PIN domain active site across all domains of life.

Senissar M, Manav MC, Brodersen DE.

Protein Sci. 2017 Aug;26(8):1474-1492. doi: 10.1002/pro.3193. Epub 2017 May 24. Review.


Higher-Order Structure in Bacterial VapBC Toxin-Antitoxin Complexes.

Bendtsen KL, Brodersen DE.

Subcell Biochem. 2017;83:381-412. doi: 10.1007/978-3-319-46503-6_14. Review.


Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding.

Bendtsen KL, Xu K, Luckmann M, Winther KS, Shah SA, Pedersen CNS, Brodersen DE.

Nucleic Acids Res. 2017 Mar 17;45(5):2875-2886. doi: 10.1093/nar/gkw1266.


The transcriptional regulator GalR self-assembles to form highly regular tubular structures.

Agerschou ED, Christiansen G, Schafer NP, Madsen DJ, Brodersen DE, Semsey S, Otzen DE.

Sci Rep. 2016 Jun 9;6:27672. doi: 10.1038/srep27672.


RRM domain of human RBM7: purification, crystallization and structure determination.

Sofos N, Winkler MB, Brodersen DE.

Acta Crystallogr F Struct Biol Commun. 2016 May;72(Pt 5):397-402. doi: 10.1107/S2053230X16006129. Epub 2016 Apr 22.


Identification of the non-ribosomal peptide synthetase responsible for biosynthesis of the potential anti-cancer drug sansalvamide in Fusarium solani.

Romans-Fuertes P, Sondergaard TE, Sandmann MI, Wollenberg RD, Nielsen KF, Hansen FT, Giese H, Brodersen DE, Sørensen JL.

Curr Genet. 2016 Nov;62(4):799-807. Epub 2016 Mar 2.


Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri.

Xu K, Dedic E, Brodersen DE.

Proteins. 2016 Jul;84(7):892-9. doi: 10.1002/prot.25002. Epub 2016 Apr 7.


Structural basis for RNA-genome recognition during bacteriophage Qβ replication.

Gytz H, Mohr D, Seweryn P, Yoshimura Y, Kutlubaeva Z, Dolman F, Chelchessa B, Chetverin AB, Mulder FA, Brodersen DE, Knudsen CR.

Nucleic Acids Res. 2015 Dec 15;43(22):10893-906. doi: 10.1093/nar/gkv1212. Epub 2015 Nov 17.


Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases.

Knudsen M, Søndergaard D, Tofting-Olesen C, Hansen FT, Brodersen DE, Pedersen CN.

Bioinformatics. 2016 Feb 1;32(3):325-9. doi: 10.1093/bioinformatics/btv600. Epub 2015 Oct 14.


Structural insights into the bacterial carbon-phosphorus lyase machinery.

Seweryn P, Van LB, Kjeldgaard M, Russo CJ, Passmore LA, Hove-Jensen B, Jochimsen B, Brodersen DE.

Nature. 2015 Sep 3;525(7567):68-72. doi: 10.1038/nature14683. Epub 2015 Aug 17.


Cut to the chase--Regulating translation through RNA cleavage.

Sofos N, Xu K, Dedic E, Brodersen DE.

Biochimie. 2015 Jul;114:10-7. doi: 10.1016/j.biochi.2015.01.009. Epub 2015 Jan 27. Review.


An update to polyketide synthase and non-ribosomal synthetase genes and nomenclature in Fusarium.

Hansen FT, Gardiner DM, Lysøe E, Fuertes PR, Tudzynski B, Wiemann P, Sondergaard TE, Giese H, Brodersen DE, Sørensen JL.

Fungal Genet Biol. 2015 Feb;75:20-9. doi: 10.1016/j.fgb.2014.12.004. Epub 2014 Dec 24. Review.


Structural characterization of the Saccharomyces cerevisiae THO complex by small-angle X-ray scattering.

Poulsen JB, Sanderson LE, Agerschou ED, Dedic E, Boesen T, Brodersen DE.

PLoS One. 2014 Jul 25;9(7):e103470. doi: 10.1371/journal.pone.0103470. eCollection 2014. Erratum in: PLoS One. 2014;9(8):e106604.


Structural analysis of the yeast exosome Rrp6p-Rrp47p complex by small-angle X-ray scattering.

Dedic E, Seweryn P, Jonstrup AT, Flygaard RK, Fedosova NU, Hoffmann SV, Boesen T, Brodersen DE.

Biochem Biophys Res Commun. 2014 Jul 18;450(1):634-40. doi: 10.1016/j.bbrc.2014.06.032. Epub 2014 Jun 14.


VapC20 of Mycobacterium tuberculosis cleaves the sarcin-ricin loop of 23S rRNA.

Winther KS, Brodersen DE, Brown AK, Gerdes K.

Nat Commun. 2013;4:2796. doi: 10.1038/ncomms3796.


Mutational analysis of the yeast RNA helicase Sub2p reveals conserved domains required for growth, mRNA export, and genomic stability.

Saguez C, Gonzales FA, Schmid M, Bøggild A, Latrick CM, Malagon F, Putnam A, Sanderson L, Jankowsky E, Brodersen DE, Jensen TH.

RNA. 2013 Oct;19(10):1363-71. doi: 10.1261/rna.040048.113. Epub 2013 Aug 20.


Mimer: an automated spreadsheet-based crystallization screening system.

Brodersen DE, Andersen GR, Andersen CB.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jul;69(Pt 7):815-20. doi: 10.1107/S1744309113014425. Epub 2013 Jun 29.


Protein expression, crystallization and preliminary X-ray crystallographic analysis of the isolated Shigella flexneri VapC toxin.

Xu K, Dedic E, Cob-Cantal P, Dienemann C, Bøggild A, Winther KS, Gerdes K, Brodersen DE.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jul;69(Pt 7):762-5. doi: 10.1107/S1744309113014012. Epub 2013 Jun 28.


The crystal structure of the intact E. coli RelBE toxin-antitoxin complex provides the structural basis for conditional cooperativity.

Bøggild A, Sofos N, Andersen KR, Feddersen A, Easter AD, Passmore LA, Brodersen DE.

Structure. 2012 Oct 10;20(10):1641-8. doi: 10.1016/j.str.2012.08.017. Epub 2012 Sep 13.


Crystal structure of the VapBC toxin-antitoxin complex from Shigella flexneri reveals a hetero-octameric DNA-binding assembly.

Dienemann C, Bøggild A, Winther KS, Gerdes K, Brodersen DE.

J Mol Biol. 2011 Dec 16;414(5):713-22. doi: 10.1016/j.jmb.2011.10.024. Epub 2011 Oct 20.


Saccharomyces cerevisiae Ngl3p is an active 3'-5' exonuclease with a specificity towards poly-A RNA reminiscent of cellular deadenylases.

Feddersen A, Dedic E, Poulsen EG, Schmid M, Van LB, Jensen TH, Brodersen DE.

Nucleic Acids Res. 2012 Jan;40(2):837-46. doi: 10.1093/nar/gkr782. Epub 2011 Sep 29.


Human 2'-phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover.

Poulsen JB, Andersen KR, Kjær KH, Durand F, Faou P, Vestergaard AL, Talbo GH, Hoogenraad N, Brodersen DE, Justesen J, Martensen PM.

Nucleic Acids Res. 2011 May;39(9):3754-70. doi: 10.1093/nar/gkq1282. Epub 2011 Jan 17.


The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE.

Neubauer C, Gao YG, Andersen KR, Dunham CM, Kelley AC, Hentschel J, Gerdes K, Ramakrishnan V, Brodersen DE.

Cell. 2009 Dec 11;139(6):1084-95. doi: 10.1016/j.cell.2009.11.015.


Cyanobacteria contain a structural homologue of the Hfq protein with altered RNA-binding properties.

Bøggild A, Overgaard M, Valentin-Hansen P, Brodersen DE.

FEBS J. 2009 Jul;276(14):3904-15.


Origins and activities of the eukaryotic exosome.

Lykke-Andersen S, Brodersen DE, Jensen TH.

J Cell Sci. 2009 May 15;122(Pt 10):1487-94. doi: 10.1242/jcs.047399. Review.


The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+ and Mn2+ in the active site.

Andersen KR, Jonstrup AT, Van LB, Brodersen DE.

RNA. 2009 May;15(5):850-61. doi: 10.1261/rna.1489409. Epub 2009 Mar 23.


Exonucleolysis is required for nuclear mRNA quality control in yeast THO mutants.

Assenholt J, Mouaikel J, Andersen KR, Brodersen DE, Libri D, Jensen TH.

RNA. 2008 Nov;14(11):2305-13. doi: 10.1261/rna.1108008. Epub 2008 Sep 29.


Take the "A" tail--quality control of ribosomal and transfer RNA.

Andersen KR, Jensen TH, Brodersen DE.

Biochim Biophys Acta. 2008 Sep;1779(9):532-7. doi: 10.1016/j.bbagrm.2008.06.011. Epub 2008 Jul 8. Review.


An Hfq-like protein in archaea: crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii.

Nielsen JS, Bøggild A, Andersen CB, Nielsen G, Boysen A, Brodersen DE, Valentin-Hansen P.

RNA. 2007 Dec;13(12):2213-23. Epub 2007 Oct 24.


The 1.4-A crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme.

Jonstrup AT, Andersen KR, Van LB, Brodersen DE.

Nucleic Acids Res. 2007;35(9):3153-64. Epub 2007 Apr 22.


Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain.

Midtgaard SF, Assenholt J, Jonstrup AT, Van LB, Jensen TH, Brodersen DE.

Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11898-903. Epub 2006 Aug 1.


Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon.

Petry S, Brodersen DE, Murphy FV 4th, Dunham CM, Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V.

Cell. 2005 Dec 29;123(7):1255-66.


The social life of ribosomal proteins.

Brodersen DE, Nissen P.

FEBS J. 2005 May;272(9):2098-108. Review.


Phasing the 30S ribosomal subunit structure.

Brodersen DE, Clemons WM Jr, Carter AP, Wimberly BT, Ramakrishnan V.

Acta Crystallogr D Biol Crystallogr. 2003 Nov;59(Pt 11):2044-50. Epub 2003 Oct 23. Review.


Atomic structures of the 30S subunit and its complexes with ligands and antibiotics.

Brodersen DE, Carter AP, Clemons WM Jr, Morgan-Warren RJ, Murphy FV 4th, Ogle JM, Tarry MJ, Wimberly BT, Ramakrishnan V.

Cold Spring Harb Symp Quant Biol. 2001;66:17-32. Review. No abstract available.


Role of 16S rRNA Helix 44 in Ribosomal Resistance to Hygromycin B.

Pfister P, Risch M, Brodersen DE, Böttger EC.

Antimicrob Agents Chemother. 2003 May;47(5):1496-502.


Shape can be seductive.

Brodersen DE, Ramakrishnan V.

Nat Struct Biol. 2003 Feb;10(2):78-80. No abstract available.


Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 S RNA.

Brodersen DE, Clemons WM Jr, Carter AP, Wimberly BT, Ramakrishnan V.

J Mol Biol. 2002 Feb 22;316(3):725-68.


Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: purification, crystallization and structure determination.

Clemons WM Jr, Brodersen DE, McCutcheon JP, May JL, Carter AP, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V.

J Mol Biol. 2001 Jul 20;310(4):827-43.


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