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Items: 1 to 50 of 62

1.

Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol.

Kim T, Stogios PJ, Khusnutdinova AN, Nemr K, Skarina T, Flick R, Joo JC, Mahadevan R, Savchenko A, Yakunin AF.

J Biol Chem. 2019 Dec 5. pii: jbc.RA119.011363. doi: 10.1074/jbc.RA119.011363. [Epub ahead of print]

2.

Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74.

Arnal G, Stogios PJ, Asohan J, Attia MA, Skarina T, Viborg AH, Henrissat B, Savchenko A, Brumer H.

J Biol Chem. 2019 Sep 6;294(36):13233-13247. doi: 10.1074/jbc.RA119.009861. Epub 2019 Jul 19.

3.

Structural enzymology reveals the molecular basis of substrate regiospecificity and processivity of an exemplar bacterial glycoside hydrolase family 74 endo-xyloglucanase.

Arnal G, Stogios PJ, Asohan J, Skarina T, Savchenko A, Brumer H.

Biochem J. 2018 Dec 19;475(24):3963-3978. doi: 10.1042/BCJ20180763.

PMID:
30463871
4.

Identification and characterization of a large family of superbinding bacterial SH2 domains.

Kaneko T, Stogios PJ, Ruan X, Voss C, Evdokimova E, Skarina T, Chung A, Liu X, Li L, Savchenko A, Ensminger AW, Li SS.

Nat Commun. 2018 Oct 31;9(1):4549. doi: 10.1038/s41467-018-06943-2.

5.

Functional diversification of the NleG effector family in enterohemorrhagic Escherichia coli.

Valleau D, Little DJ, Borek D, Skarina T, Quaile AT, Di Leo R, Houliston S, Lemak A, Arrowsmith CH, Coombes BK, Savchenko A.

Proc Natl Acad Sci U S A. 2018 Oct 2;115(40):10004-10009. doi: 10.1073/pnas.1718350115. Epub 2018 Sep 14.

6.

The evolution of substrate discrimination in macrolide antibiotic resistance enzymes.

Pawlowski AC, Stogios PJ, Koteva K, Skarina T, Evdokimova E, Savchenko A, Wright GD.

Nat Commun. 2018 Jan 9;9(1):112. doi: 10.1038/s41467-017-02680-0.

7.

Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes.

Xu Z, Stogios PJ, Quaile AT, Forsberg KJ, Patel S, Skarina T, Houliston S, Arrowsmith C, Dantas G, Savchenko A.

ACS Infect Dis. 2017 Sep 8;3(9):653-665. doi: 10.1021/acsinfecdis.7b00068. Epub 2017 Aug 16.

PMID:
28756664
8.

Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families.

Popovic A, Hai T, Tchigvintsev A, Hajighasemi M, Nocek B, Khusnutdinova AN, Brown G, Glinos J, Flick R, Skarina T, Chernikova TN, Yim V, Brüls T, Paslier DL, Yakimov MM, Joachimiak A, Ferrer M, Golyshina OV, Savchenko A, Golyshin PN, Yakunin AF.

Sci Rep. 2017 Mar 8;7:44103. doi: 10.1038/srep44103.

9.

Rifampin phosphotransferase is an unusual antibiotic resistance kinase.

Stogios PJ, Cox G, Spanogiannopoulos P, Pillon MC, Waglechner N, Skarina T, Koteva K, Guarné A, Savchenko A, Wright GD.

Nat Commun. 2016 Apr 22;7:11343. doi: 10.1038/ncomms11343.

10.

Legionella pneumophila S1P-lyase targets host sphingolipid metabolism and restrains autophagy.

Rolando M, Escoll P, Nora T, Botti J, Boitez V, Bedia C, Daniels C, Abraham G, Stogios PJ, Skarina T, Christophe C, Dervins-Ravault D, Cazalet C, Hilbi H, Rupasinghe TW, Tull D, McConville MJ, Ong SY, Hartland EL, Codogno P, Levade T, Naderer T, Savchenko A, Buchrieser C.

Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):1901-6. doi: 10.1073/pnas.1522067113. Epub 2016 Feb 1.

11.

Identification of Salmonella Typhimurium Deubiquitinase SseL Substrates by Immunoaffinity Enrichment and Quantitative Proteomic Analysis.

Nakayasu ES, Sydor MA, Brown RN, Sontag RL, Sobreira TJ, Slysz GW, Humphrys DR, Skarina T, Onoprienko O, Di Leo R, Deatherage Kaiser BL, Li J, Ansong C, Cambronne ED, Smith RD, Savchenko A, Adkins JN.

J Proteome Res. 2015 Sep 4;14(9):4029-38. doi: 10.1021/acs.jproteome.5b00574. Epub 2015 Aug 6.

12.

Molecular Characterization of LubX: Functional Divergence of the U-Box Fold by Legionella pneumophila.

Quaile AT, Urbanus ML, Stogios PJ, Nocek B, Skarina T, Ensminger AW, Savchenko A.

Structure. 2015 Aug 4;23(8):1459-1469. doi: 10.1016/j.str.2015.05.020. Epub 2015 Jul 2.

13.

Electroporation of functional bacterial effectors into mammalian cells.

Sontag RL, Mihai C, Orr G, Savchenko A, Skarina T, Cui H, Cort JR, Adkins JN, Brown RN.

J Vis Exp. 2015 Jan 19;(95):52296. doi: 10.3791/52296.

14.

The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity.

Lemak S, Nocek B, Beloglazova N, Skarina T, Flick R, Brown G, Joachimiak A, Savchenko A, Yakunin AF.

Nucleic Acids Res. 2014;42(17):11144-55. doi: 10.1093/nar/gku797. Epub 2014 Sep 8.

15.

Type III effector NleH2 from Escherichia coli O157:H7 str. Sakai features an atypical protein kinase domain.

Halavaty AS, Anderson SM, Wawrzak Z, Kudritska M, Skarina T, Anderson WF, Savchenko A.

Biochemistry. 2014 Apr 22;53(15):2433-5. doi: 10.1021/bi500016j. Epub 2014 Apr 10.

PMID:
24712300
16.

High-throughput crystallization screening.

Skarina T, Xu X, Evdokimova E, Savchenko A.

Methods Mol Biol. 2014;1140:159-68. doi: 10.1007/978-1-4939-0354-2_12.

PMID:
24590716
17.

Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus.

Lemak S, Beloglazova N, Nocek B, Skarina T, Flick R, Brown G, Popovic A, Joachimiak A, Savchenko A, Yakunin AF.

J Am Chem Soc. 2013 Nov 20;135(46):17476-87. doi: 10.1021/ja408729b. Epub 2013 Nov 11.

18.

Structure of isochorismate synthase DhbC from Bacillus anthracis.

Domagalski MJ, Tkaczuk KL, Chruszcz M, Skarina T, Onopriyenko O, Cymborowski M, Grabowski M, Savchenko A, Minor W.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Sep;69(Pt 9):956-61. doi: 10.1107/S1744309113021246. Epub 2013 Aug 19.

19.

The Legionella pneumophila kai operon is implicated in stress response and confers fitness in competitive environments.

Loza-Correa M, Sahr T, Rolando M, Daniels C, Petit P, Skarina T, Gomez Valero L, Dervins-Ravault D, Honoré N, Savchenko A, Buchrieser C.

Environ Microbiol. 2014 Feb;16(2):359-81. doi: 10.1111/1462-2920.12223. Epub 2013 Aug 19.

20.

A pathogen type III effector with a novel E3 ubiquitin ligase architecture.

Singer AU, Schulze S, Skarina T, Xu X, Cui H, Eschen-Lippold L, Egler M, Srikumar T, Raught B, Lee J, Scheel D, Savchenko A, Bonas U.

PLoS Pathog. 2013 Jan;9(1):e1003121. doi: 10.1371/journal.ppat.1003121. Epub 2013 Jan 24. Erratum in: PLoS Pathog. 2013 May 7;9(5):.

21.

Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria.

Halavaty AS, Kim Y, Minasov G, Shuvalova L, Dubrovska I, Winsor J, Zhou M, Onopriyenko O, Skarina T, Papazisi L, Kwon K, Peterson SN, Joachimiak A, Savchenko A, Anderson WF.

Acta Crystallogr D Biol Crystallogr. 2012 Oct;68(Pt 10):1359-70. Epub 2012 Sep 13.

22.

Structure of a short-chain dehydrogenase/reductase from Bacillus anthracis.

Hou J, Wojciechowska K, Zheng H, Chruszcz M, Cooper DR, Cymborowski M, Skarina T, Gordon E, Luo H, Savchenko A, Minor W.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Jun 1;68(Pt 6):632-7. doi: 10.1107/S1744309112017939. Epub 2012 May 24.

23.

Structural analysis of HopPmaL reveals the presence of a second adaptor domain common to the HopAB family of Pseudomonas syringae type III effectors.

Singer AU, Wu B, Yee A, Houliston S, Xu X, Cui H, Skarina T, Garcia M, Semesi A, Arrowsmith CH, Savchenko A.

Biochemistry. 2012 Jan 10;51(1):1-3. doi: 10.1021/bi2013883. Epub 2011 Dec 28.

24.

A specific inorganic triphosphatase from Nitrosomonas europaea: structure and catalytic mechanism.

Delvaux D, Murty MR, Gabelica V, Lakaye B, Lunin VV, Skarina T, Onopriyenko O, Kohn G, Wins P, De Pauw E, Bettendorff L.

J Biol Chem. 2011 Sep 30;286(39):34023-35. doi: 10.1074/jbc.M111.233585. Epub 2011 Aug 12.

25.

Structural analysis of a putative aminoglycoside N-acetyltransferase from Bacillus anthracis.

Klimecka MM, Chruszcz M, Font J, Skarina T, Shumilin I, Onopryienko O, Porebski PJ, Cymborowski M, Zimmerman MD, Hasseman J, Glomski IJ, Lebioda L, Savchenko A, Edwards A, Minor W.

J Mol Biol. 2011 Jul 15;410(3):411-23. doi: 10.1016/j.jmb.2011.04.076. Epub 2011 May 13.

26.

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.

Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF.

Mol Microbiol. 2011 Jan;79(2):484-502. doi: 10.1111/j.1365-2958.2010.07465.x. Epub 2010 Dec 7.

27.

NleG Type 3 effectors from enterohaemorrhagic Escherichia coli are U-Box E3 ubiquitin ligases.

Wu B, Skarina T, Yee A, Jobin MC, Dileo R, Semesi A, Fares C, Lemak A, Coombes BK, Arrowsmith CH, Singer AU, Savchenko A.

PLoS Pathog. 2010 Jun 24;6(6):e1000960. doi: 10.1371/journal.ppat.1000960.

28.

Structure and protein-protein interaction studies on Chlamydia trachomatis protein CT670 (YscO Homolog).

Lorenzini E, Singer A, Singh B, Lam R, Skarina T, Chirgadze NY, Savchenko A, Gupta RS.

J Bacteriol. 2010 Jun;192(11):2746-56. doi: 10.1128/JB.01479-09. Epub 2010 Mar 26.

29.

Crystal structure and molecular modeling study of N-carbamoylsarcosine amidase Ta0454 from Thermoplasma acidophilum.

Luo HB, Zheng H, Zimmerman MD, Chruszcz M, Skarina T, Egorova O, Savchenko A, Edwards AM, Minor W.

J Struct Biol. 2010 Mar;169(3):304-11. doi: 10.1016/j.jsb.2009.11.008. Epub 2009 Nov 20.

30.

The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold.

Wang S, Kirillova O, Chruszcz M, Gront D, Zimmerman MD, Cymborowski MT, Shumilin IA, Skarina T, Gorodichtchenskaia E, Savchenko A, Edwards AM, Minor W.

Protein Sci. 2009 Nov;18(11):2410-9. doi: 10.1002/pro.251.

31.

ADP-dependent 6-phosphofructokinase from Pyrococcus horikoshii OT3: structure determination and biochemical characterization of PH1645.

Currie MA, Merino F, Skarina T, Wong AH, Singer A, Brown G, Savchenko A, Caniuguir A, Guixé V, Yakunin AF, Jia Z.

J Biol Chem. 2009 Aug 21;284(34):22664-71. doi: 10.1074/jbc.M109.012401. Epub 2009 Jun 24.

32.

The long-chain fatty acid sensor, PsrA, modulates the expression of rpoS and the type III secretion exsCEBA operon in Pseudomonas aeruginosa.

Kang Y, Lunin VV, Skarina T, Savchenko A, Schurr MJ, Hoang TT.

Mol Microbiol. 2009 Jul;73(1):120-36. doi: 10.1111/j.1365-2958.2009.06757.x. Epub 2009 Jun 8.

33.

Structural and biochemical characterization of the type II fructose-1,6-bisphosphatase GlpX from Escherichia coli.

Brown G, Singer A, Lunin VV, Proudfoot M, Skarina T, Flick R, Kochinyan S, Sanishvili R, Joachimiak A, Edwards AM, Savchenko A, Yakunin AF.

J Biol Chem. 2009 Feb 6;284(6):3784-92. doi: 10.1074/jbc.M808186200. Epub 2008 Dec 10.

34.

Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases.

Singer AU, Rohde JR, Lam R, Skarina T, Kagan O, Dileo R, Chirgadze NY, Cuff ME, Joachimiak A, Tyers M, Sansonetti PJ, Parsot C, Savchenko A.

Nat Struct Mol Biol. 2008 Dec;15(12):1293-301. doi: 10.1038/nsmb.1511. Epub 2008 Nov 9.

35.

Functional and structural characterization of four glutaminases from Escherichia coli and Bacillus subtilis.

Brown G, Singer A, Proudfoot M, Skarina T, Kim Y, Chang C, Dementieva I, Kuznetsova E, Gonzalez CF, Joachimiak A, Savchenko A, Yakunin AF.

Biochemistry. 2008 May 27;47(21):5724-35. doi: 10.1021/bi800097h. Epub 2008 May 6.

36.

In situ proteolysis for protein crystallization and structure determination.

Dong A, Xu X, Edwards AM; Midwest Center for Structural Genomics; Structural Genomics Consortium, Chang C, Chruszcz M, Cuff M, Cymborowski M, Di Leo R, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P Jr, Flodin S, Flores A, Gräslund S, Hammerström M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H.

Nat Methods. 2007 Dec;4(12):1019-21. Epub 2007 Nov 4.

37.

Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli.

Savchenko A, Proudfoot M, Skarina T, Singer A, Litvinova O, Sanishvili R, Brown G, Chirgadze N, Yakunin AF.

J Mol Biol. 2007 Dec 7;374(4):1091-103. Epub 2007 Oct 11.

PMID:
17976651
38.

Crystal structures of TM0549 and NE1324--two orthologs of E. coli AHAS isozyme III small regulatory subunit.

Petkowski JJ, Chruszcz M, Zimmerman MD, Zheng H, Skarina T, Onopriyenko O, Cymborowski MT, Koclega KD, Savchenko A, Edwards A, Minor W.

Protein Sci. 2007 Jul;16(7):1360-7.

39.

Crystal structure of RNase T, an exoribonuclease involved in tRNA maturation and end turnover.

Zuo Y, Zheng H, Wang Y, Chruszcz M, Cymborowski M, Skarina T, Savchenko A, Malhotra A, Minor W.

Structure. 2007 Apr;15(4):417-28.

40.

An extremely SAD case: structure of a putative redox-enzyme maturation protein from Archaeoglobus fulgidus at 3.4 A resolution.

Kirillova O, Chruszcz M, Shumilin IA, Skarina T, Gorodichtchenskaia E, Cymborowski M, Savchenko A, Edwards A, Minor W.

Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):348-54. Epub 2007 Feb 21.

PMID:
17327672
41.

Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure.

Lesnyak DV, Osipiuk J, Skarina T, Sergiev PV, Bogdanov AA, Edwards A, Savchenko A, Joachimiak A, Dontsova OA.

J Biol Chem. 2007 Feb 23;282(8):5880-7. Epub 2006 Dec 21.

42.

Structural characterization of GntR/HutC family signaling domain.

Gorelik M, Lunin VV, Skarina T, Savchenko A.

Protein Sci. 2006 Jun;15(6):1506-11. Epub 2006 May 2.

43.

Structure of SAICAR synthase from Thermotoga maritima at 2.2 angstroms reveals an unusual covalent dimer.

Zhang R, Skarina T, Evdokimova E, Edwards A, Savchenko A, Laskowski R, Cuff ME, Joachimiak A.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Apr 1;62(Pt 4):335-9. Epub 2006 Mar 25.

44.

Structural and biochemical study of effector molecule recognition by the E.coli glyoxylate and allantoin utilization regulatory protein AllR.

Walker JR, Altamentova S, Ezersky A, Lorca G, Skarina T, Kudritska M, Ball LJ, Bochkarev A, Savchenko A.

J Mol Biol. 2006 May 5;358(3):810-28. Epub 2006 Mar 3.

PMID:
16546208
45.

NMR and X-ray crystallography, complementary tools in structural proteomics of small proteins.

Yee AA, Savchenko A, Ignachenko A, Lukin J, Xu X, Skarina T, Evdokimova E, Liu CS, Semesi A, Guido V, Edwards AM, Arrowsmith CH.

J Am Chem Soc. 2005 Nov 30;127(47):16512-7.

PMID:
16305238
46.

The X-ray crystal structure of PA3566 from Pseudomonas aureginosa at 1.8 A resolution.

Sanders DA, Walker JR, Skarina T, Savchenko A.

Proteins. 2005 Oct 1;61(1):209-12. No abstract available.

PMID:
16049913
47.

Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.

Blankenfeldt W, Kuzin AP, Skarina T, Korniyenko Y, Tong L, Bayer P, Janning P, Thomashow LS, Mavrodi DV.

Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16431-6. Epub 2004 Nov 15.

48.

The crystal structure of Escherichia coli MoaB suggests a probable role in molybdenum cofactor synthesis.

Sanishvili R, Beasley S, Skarina T, Glesne D, Joachimiak A, Edwards A, Savchenko A.

J Biol Chem. 2004 Oct 1;279(40):42139-46. Epub 2004 Jul 21.

49.

X-ray crystal structure of CutA from Thermotoga maritima at 1.4 A resolution.

Savchenko A, Skarina T, Evdokimova E, Watson JD, Laskowski R, Arrowsmith CH, Edwards AM, Joachimiak A, Zhang RG.

Proteins. 2004 Jan 1;54(1):162-5. No abstract available.

50.

The 2.2 A resolution structure of RpiB/AlsB from Escherichia coli illustrates a new approach to the ribose-5-phosphate isomerase reaction.

Zhang RG, Andersson CE, Skarina T, Evdokimova E, Edwards AM, Joachimiak A, Savchenko A, Mowbray SL.

J Mol Biol. 2003 Oct 3;332(5):1083-94.

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