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Items: 46

1.

Aspartate/asparagine-β-hydroxylase crystal structures reveal an unexpected epidermal growth factor-like domain substrate disulfide pattern.

Pfeffer I, Brewitz L, Krojer T, Jensen SA, Kochan GT, Kershaw NJ, Hewitson KS, McNeill LA, Kramer H, Münzel M, Hopkinson RJ, Oppermann U, Handford PA, McDonough MA, Schofield CJ.

Nat Commun. 2019 Oct 28;10(1):4910. doi: 10.1038/s41467-019-12711-7.

2.

Rapid Covalent-Probe Discovery by Electrophile-Fragment Screening.

Resnick E, Bradley A, Gan J, Douangamath A, Krojer T, Sethi R, Geurink PP, Aimon A, Amitai G, Bellini D, Bennett J, Fairhead M, Fedorov O, Gabizon R, Gan J, Guo J, Plotnikov A, Reznik N, Ruda GF, Díaz-Sáez L, Straub VM, Szommer T, Velupillai S, Zaidman D, Zhang Y, Coker AR, Dowson CG, Barr HM, Wang C, Huber KVM, Brennan PE, Ovaa H, von Delft F, London N.

J Am Chem Soc. 2019 Jun 5;141(22):8951-8968. doi: 10.1021/jacs.9b02822. Epub 2019 May 22.

3.

A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase.

Pfeiffer M, Johansson C, Krojer T, Kavanagh KL, Oppermann U, Nidetzky B.

ACS Catal. 2019 Apr 5;9(4):2962-2968. doi: 10.1021/acscatal.9b00064. Epub 2019 Mar 1.

4.

Achieving a Good Crystal System for Crystallographic X-Ray Fragment Screening.

Collins PM, Douangamath A, Talon R, Dias A, Brandao-Neto J, Krojer T, von Delft F.

Methods Enzymol. 2018;610:251-264. doi: 10.1016/bs.mie.2018.09.027. Epub 2018 Oct 15.

PMID:
30390801
5.

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.

Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F.

Nat Commun. 2017 Apr 24;8:15123. doi: 10.1038/ncomms15123.

6.

Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites.

Pearce NM, Bradley AR, Krojer T, Marsden BD, Deane CM, von Delft F.

Struct Dyn. 2017 Feb 28;4(3):032104. doi: 10.1063/1.4974176. eCollection 2017 May.

7.

The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination.

Krojer T, Talon R, Pearce N, Collins P, Douangamath A, Brandao-Neto J, Dias A, Marsden B, von Delft F.

Acta Crystallogr D Struct Biol. 2017 Mar 1;73(Pt 3):267-278. doi: 10.1107/S2059798316020234. Epub 2017 Feb 24.

8.

Proper modelling of ligand binding requires an ensemble of bound and unbound states.

Pearce NM, Krojer T, von Delft F.

Acta Crystallogr D Struct Biol. 2017 Mar 1;73(Pt 3):256-266. doi: 10.1107/S2059798317003412. Epub 2017 Mar 6.

9.

Gentle, fast and effective crystal soaking by acoustic dispensing.

Collins PM, Ng JT, Talon R, Nekrosiute K, Krojer T, Douangamath A, Brandao-Neto J, Wright N, Pearce NM, von Delft F.

Acta Crystallogr D Struct Biol. 2017 Mar 1;73(Pt 3):246-255. doi: 10.1107/S205979831700331X. Epub 2017 Mar 6.

10.

Structure and inhibitor specificity of the PCTAIRE-family kinase CDK16.

Dixon-Clarke SE, Shehata SN, Krojer T, Sharpe TD, von Delft F, Sakamoto K, Bullock AN.

Biochem J. 2017 Feb 20;474(5):699-713. doi: 10.1042/BCJ20160941.

11.

Multivalent Histone and DNA Engagement by a PHD/BRD/PWWP Triple Reader Cassette Recruits ZMYND8 to K14ac-Rich Chromatin.

Savitsky P, Krojer T, Fujisawa T, Lambert JP, Picaud S, Wang CY, Shanle EK, Krajewski K, Friedrichsen H, Kanapin A, Goding C, Schapira M, Samsonova A, Strahl BD, Gingras AC, Filippakopoulos P.

Cell Rep. 2016 Dec 6;17(10):2724-2737. doi: 10.1016/j.celrep.2016.11.014.

12.

Mechanism of TAp73 inhibition by ΔNp63 and structural basis of p63/p73 hetero-tetramerization.

Gebel J, Luh LM, Coutandin D, Osterburg C, Löhr F, Schäfer B, Frombach AS, Sumyk M, Buchner L, Krojer T, Salah E, Mathea S, Güntert P, Knapp S, Dötsch V.

Cell Death Differ. 2016 Dec;23(12):1930-1940. doi: 10.1038/cdd.2016.83. Epub 2016 Oct 7.

13.

A generic protocol for protein crystal dehydration using the HC1b humidity controller.

Lobley CM, Sandy J, Sanchez-Weatherby J, Mazzorana M, Krojer T, Nowak RP, Sorensen TL.

Acta Crystallogr D Struct Biol. 2016 May;72(Pt 5):629-40. doi: 10.1107/S2059798316003065. Epub 2016 Apr 26.

14.

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J.

Structure. 2016 Apr 5;24(4):502-508. doi: 10.1016/j.str.2016.02.017.

15.

An overview of heavy-atom derivatization of protein crystals.

Pike AC, Garman EF, Krojer T, von Delft F, Carpenter EP.

Acta Crystallogr D Struct Biol. 2016 Mar;72(Pt 3):303-18. doi: 10.1107/S2059798316000401. Epub 2016 Mar 1. Review.

16.

A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain.

Cox OB, Krojer T, Collins P, Monteiro O, Talon R, Bradley A, Fedorov O, Amin J, Marsden BD, Spencer J, von Delft F, Brennan PE.

Chem Sci. 2016 Mar 1;7(3):2322-2330. doi: 10.1039/c5sc03115j. Epub 2015 Dec 22.

17.

8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.

Bavetsias V, Lanigan RM, Ruda GF, Atrash B, McLaughlin MG, Tumber A, Mok NY, Le Bihan YV, Dempster S, Boxall KJ, Jeganathan F, Hatch SB, Savitsky P, Velupillai S, Krojer T, England KS, Sejberg J, Thai C, Donovan A, Pal A, Scozzafava G, Bennett JM, Kawamura A, Johansson C, Szykowska A, Gileadi C, Burgess-Brown NA, von Delft F, Oppermann U, Walters Z, Shipley J, Raynaud FI, Westaway SM, Prinjha RK, Fedorov O, Burke R, Schofield CJ, Westwood IM, Bountra C, Müller S, van Montfort RL, Brennan PE, Blagg J.

J Med Chem. 2016 Feb 25;59(4):1388-409. doi: 10.1021/acs.jmedchem.5b01635. Epub 2016 Jan 7.

18.

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.

19.

Human ISPD Is a Cytidyltransferase Required for Dystroglycan O-Mannosylation.

Riemersma M, Froese DS, van Tol W, Engelke UF, Kopec J, van Scherpenzeel M, Ashikov A, Krojer T, von Delft F, Tessari M, Buczkowska A, Swiezewska E, Jae LT, Brummelkamp TR, Manya H, Endo T, van Bokhoven H, Yue WW, Lefeber DJ.

Chem Biol. 2015 Dec 17;22(12):1643-52. doi: 10.1016/j.chembiol.2015.10.014. Epub 2015 Dec 10.

20.

Optimisation of a triazolopyridine based histone demethylase inhibitor yields a potent and selective KDM2A (FBXL11) inhibitor.

England KS, Tumber A, Krojer T, Scozzafava G, Ng SS, Daniel M, Szykowska A, Che K, von Delft F, Burgess-Brown NA, Kawamura A, Schofield CJ, Brennan PE.

Medchemcomm. 2014 Dec 1;5(12):1879-1886. doi: 10.1039/C4MD00291A.

21.

Structural basis of glycogen branching enzyme deficiency and pharmacologic rescue by rational peptide design.

Froese DS, Michaeli A, McCorvie TJ, Krojer T, Sasi M, Melaev E, Goldblum A, Zatsepin M, Lossos A, Álvarez R, Escribá PV, Minassian BA, von Delft F, Kakhlon O, Yue WW.

Hum Mol Genet. 2015 Oct 15;24(20):5667-76. doi: 10.1093/hmg/ddv280. Epub 2015 Jul 21.

22.

Lysine methylation-dependent binding of 53BP1 to the pRb tumor suppressor.

Carr SM, Munro S, Zalmas LP, Fedorov O, Johansson C, Krojer T, Sagum CA, Bedford MT, Oppermann U, La Thangue NB.

Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11341-6. doi: 10.1073/pnas.1403737111. Epub 2014 Jul 21.

23.

Ribosomal oxygenases are structurally conserved from prokaryotes to humans.

Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JRC, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ.

Nature. 2014 Jun 19;510(7505):422-426. doi: 10.1038/nature13263. Epub 2014 May 11.

24.

5-Carboxy-8-hydroxyquinoline is a Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor which Causes Iron Translocation.

Hopkinson RJ, Tumber A, Yapp C, Chowdhury R, Aik W, Che KH, Li XS, Kristensen JBL, King ONF, Chan MC, Yeoh KK, Choi H, Walport LJ, Thinnes CC, Bush JT, Lejeune C, Rydzik AM, Rose NR, Bagg EA, McDonough MA, Krojer T, Yue WW, Ng SS, Olsen L, Brennan PE, Oppermann U, Muller-Knapp S, Klose RJ, Ratcliffe PJ, Schofield CJ, Kawamura A.

Chem Sci. 2013 Aug 1;4(8):3110-3117. doi: 10.1039/C3SC51122G.

25.

Squeezing the most from every crystal: the fine details of data collection.

Krojer T, Pike AC, von Delft F.

Acta Crystallogr D Biol Crystallogr. 2013 Jul;69(Pt 7):1303-13. doi: 10.1107/S0907444913013280. Epub 2013 Jun 18.

26.

Crystal structures of malonyl-coenzyme A decarboxylase provide insights into its catalytic mechanism and disease-causing mutations.

Froese DS, Forouhar F, Tran TH, Vollmar M, Kim YS, Lew S, Neely H, Seetharaman J, Shen Y, Xiao R, Acton TB, Everett JK, Cannone G, Puranik S, Savitsky P, Krojer T, Pilka ES, Kiyani W, Lee WH, Marsden BD, von Delft F, Allerston CK, Spagnolo L, Gileadi O, Montelione GT, Oppermann U, Yue WW, Tong L.

Structure. 2013 Jul 2;21(7):1182-92. doi: 10.1016/j.str.2013.05.001. Epub 2013 Jun 20.

27.

Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases.

Canning P, Cooper CD, Krojer T, Murray JW, Pike AC, Chaikuad A, Keates T, Thangaratnarajah C, Hojzan V, Ayinampudi V, Marsden BD, Gileadi O, Knapp S, von Delft F, Bullock AN.

J Biol Chem. 2013 Mar 15;288(11):7803-14. doi: 10.1074/jbc.M112.437996. Epub 2013 Jan 24. Erratum in: J Biol Chem. 2013 Sep 27;388(39):28304. Ayinampudi, Vikram [added].

28.

Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases.

Rose NR, Woon EC, Tumber A, Walport LJ, Chowdhury R, Li XS, King ON, Lejeune C, Ng SS, Krojer T, Chan MC, Rydzik AM, Hopkinson RJ, Che KH, Daniel M, Strain-Damerell C, Gileadi C, Kochan G, Leung IK, Dunford J, Yeoh KK, Ratcliffe PJ, Burgess-Brown N, von Delft F, Muller S, Marsden B, Brennan PE, McDonough MA, Oppermann U, Klose RJ, Schofield CJ, Kawamura A.

J Med Chem. 2012 Jul 26;55(14):6639-43. doi: 10.1021/jm300677j. Epub 2012 Jul 11.

29.

Structure of MMACHC reveals an arginine-rich pocket and a domain-swapped dimer for its B12 processing function.

Froese DS, Krojer T, Wu X, Shrestha R, Kiyani W, von Delft F, Gravel RA, Oppermann U, Yue WW.

Biochemistry. 2012 Jun 26;51(25):5083-90. doi: 10.1021/bi300150y. Epub 2012 Jun 14.

PMID:
22642810
30.

Molecular adaptation of the DegQ protease to exert protein quality control in the bacterial cell envelope.

Sawa J, Malet H, Krojer T, Canellas F, Ehrmann M, Clausen T.

J Biol Chem. 2011 Sep 2;286(35):30680-90. doi: 10.1074/jbc.M111.243832. Epub 2011 Jun 17.

31.

Assessment of radiation damage behaviour in a large collection of empirically optimized datasets highlights the importance of unmeasured complicating effects.

Krojer T, von Delft F.

J Synchrotron Radiat. 2011 May;18(Pt 3):387-97. doi: 10.1107/S0909049511008235. Epub 2011 Apr 9.

32.

Crystal structures of the endoplasmic reticulum aminopeptidase-1 (ERAP1) reveal the molecular basis for N-terminal peptide trimming.

Kochan G, Krojer T, Harvey D, Fischer R, Chen L, Vollmar M, von Delft F, Kavanagh KL, Brown MA, Bowness P, Wordsworth P, Kessler BM, Oppermann U.

Proc Natl Acad Sci U S A. 2011 May 10;108(19):7745-50. doi: 10.1073/pnas.1101262108. Epub 2011 Apr 20.

33.

Substrate-induced remodeling of the active site regulates human HTRA1 activity.

Truebestein L, Tennstaedt A, Mönig T, Krojer T, Canellas F, Kaiser M, Clausen T, Ehrmann M.

Nat Struct Mol Biol. 2011 Mar;18(3):386-8. doi: 10.1038/nsmb.2013. Epub 2011 Feb 6.

PMID:
21297635
34.

Structural and mechanistic studies on γ-butyrobetaine hydroxylase.

Leung IK, Krojer TJ, Kochan GT, Henry L, von Delft F, Claridge TD, Oppermann U, McDonough MA, Schofield CJ.

Chem Biol. 2010 Dec 22;17(12):1316-24. doi: 10.1016/j.chembiol.2010.09.016.

35.

Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6.

Mantri M, Krojer T, Bagg EA, Webby CA, Butler DS, Kochan G, Kavanagh KL, Oppermann U, McDonough MA, Schofield CJ.

J Mol Biol. 2010 May 31. [Epub ahead of print]

PMID:
20685276
36.

Crystal structure of the 2-oxoglutarate- and Fe(II)-dependent lysyl hydroxylase JMJD6.

Mantri M, Krojer T, Bagg EA, Webby CJ, Butler DS, Kochan G, Kavanagh KL, Oppermann U, McDonough MA, Schofield CJ.

J Mol Biol. 2010 Aug 13;401(2):211-22.

PMID:
20684070
37.

HtrA proteases have a conserved activation mechanism that can be triggered by distinct molecular cues.

Krojer T, Sawa J, Huber R, Clausen T.

Nat Struct Mol Biol. 2010 Jul;17(7):844-52. doi: 10.1038/nsmb.1840. Epub 2010 Jun 27.

PMID:
20581825
38.

Structure, function and regulation of the conserved serine proteases DegP and DegS of Escherichia coli.

Meltzer M, Hasenbein S, Mamant N, Merdanovic M, Poepsel S, Hauske P, Kaiser M, Huber R, Krojer T, Clausen T, Ehrmann M.

Res Microbiol. 2009 Nov;160(9):660-6. doi: 10.1016/j.resmic.2009.07.012. Epub 2009 Aug 18. Review.

PMID:
19695325
39.

Selectivity profiling of DegP substrates and inhibitors.

Hauske P, Meltzer M, Ottmann C, Krojer T, Clausen T, Ehrmann M, Kaiser M.

Bioorg Med Chem. 2009 Apr 1;17(7):2920-4. doi: 10.1016/j.bmc.2009.01.073. Epub 2009 Feb 5.

PMID:
19233659
40.

Interplay of PDZ and protease domain of DegP ensures efficient elimination of misfolded proteins.

Krojer T, Pangerl K, Kurt J, Sawa J, Stingl C, Mechtler K, Huber R, Ehrmann M, Clausen T.

Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7702-7. doi: 10.1073/pnas.0803392105. Epub 2008 May 27.

41.

Structural basis for the regulated protease and chaperone function of DegP.

Krojer T, Sawa J, Schäfer E, Saibil HR, Ehrmann M, Clausen T.

Nature. 2008 Jun 12;453(7197):885-90. doi: 10.1038/nature07004. Epub 2008 May 21.

PMID:
18496527
42.

Allosteric activation of HtrA protease DegP by stress signals during bacterial protein quality control.

Meltzer M, Hasenbein S, Hauske P, Kucz N, Merdanovic M, Grau S, Beil A, Jones D, Krojer T, Clausen T, Ehrmann M, Kaiser M.

Angew Chem Int Ed Engl. 2008;47(7):1332-4. doi: 10.1002/anie.200703273. No abstract available.

PMID:
18175296
43.

Regulation of the sigmaE stress response by DegS: how the PDZ domain keeps the protease inactive in the resting state and allows integration of different OMP-derived stress signals upon folding stress.

Hasselblatt H, Kurzbauer R, Wilken C, Krojer T, Sawa J, Kurt J, Kirk R, Hasenbein S, Ehrmann M, Clausen T.

Genes Dev. 2007 Oct 15;21(20):2659-70.

44.

Biosynthesis of riboflavin: structure and properties of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase of Methanocaldococcus jannaschii.

Chatwell L, Krojer T, Fidler A, Römisch W, Eisenreich W, Bacher A, Huber R, Fischer M.

J Mol Biol. 2006 Jun 23;359(5):1334-51. Epub 2006 May 6.

PMID:
16730025
45.

Crystal structure of an archaeal pentameric riboflavin synthase in complex with a substrate analog inhibitor: stereochemical implications.

Ramsperger A, Augustin M, Schott AK, Gerhardt S, Krojer T, Eisenreich W, Illarionov B, Cushman M, Bacher A, Huber R, Fischer M.

J Biol Chem. 2006 Jan 13;281(2):1224-32. Epub 2005 Nov 4.

46.

Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine.

Krojer T, Garrido-Franco M, Huber R, Ehrmann M, Clausen T.

Nature. 2002 Mar 28;416(6879):455-9. Erratum in: Nature 2002 May 2;417(6884):102.

PMID:
11919638

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