Publications by the Berghuis Lab

1. Yachnin, B. J., Colin, D. Y., Volpato, J. P., Ebert, M., Pelletier, J. N., Berghuis, A. M. (2011) Novel crystallization conditions for tandem variant R67 DHFR yield a wild-type crystal structure, Acta Crystallogr Sect F Struct Biol Cryst Commun 67, 1316-1322

2. Shi, K., Houston, D. R., Berghuis, A. M. (2011) Crystal structures of antibiotic-bound complexes of aminoglycoside 2"-phosphotransferase IVa highlight the diversity in substrate binding modes among aminoglycoside kinases, Biochemistry 50, 6237-6244

3. Fong, D. H., Xiong, B., Hwang, J., Berghuis, A. M. (2011) Crystal structures of two aminoglycoside kinases bound with a eukaryotic protein kinase inhibitor, PLoS One 6, e19589

4. Freiburger, L. A., Baettig, O. M., Sprules, T., Berghuis, A. M., Auclair, K., Mittermaier, A. K. (2011) Competing allosteric mechanisms modulate substrate binding in a dimeric enzyme, Nat Struct Mol Biol 18, 288-294

5. Zang, Z., Mui, M. Z., Chan, F., Roopchand, D. E., Marcellus, R. C., Blanchette, P., Li, S., Berghuis, A. M. Branton, P. E. (2011) Genetic analysis of B55alpha/Cdc55 protein phosphatase 2A subunits: association with the adenovirus E4orf4 protein, J Virol 85, 286-295

6. Gomez, M. A., Alisaraie, L., Shio, M. T., Berghuis, A. M., Lebrun, C., Gautier-Luneau, I., Olivier, M. (2010) Protein tyrosine phosphatases are regulated by mononuclear iron dicitrate, J Biol Chem 285, 24620-24628

7. Fong, D. H., Lemke, C. T., Hwang, J., Xiong, B., Berghuis, A. M. (2010) Structure of the antibiotic resistance factor spectinomycin phosphotransferase from Legionella pneumophila, J Biol Chem 285, 9545-9555

8. Hosokawa, N., Tremblay, L. O., Sleno, B., Kamiya, Y., Wada, I., Nagata, K., Kato, K., Herscovics, A. (2010) EDEM1 accelerates the trimming of alpha1,2-linked mannose on the C branch of N-glycans, Glycobiology 20, 567-575

9. Volpato, J. P., Yachnin, B. J., Blanchet, J., Guerrero, V., Poulin, L., Fossati, E., Berghuis, A. M., Pelletier, J. N. (2009) Multiple conformers in active site of human dihydrofolate reductase F31R/Q35E double mutant suggest structural basis for methotrexate resistance, J Biol Chem 284, 20079-20089.

10. Fong, D.H., Berghuis, A. M. (2009) Structural basis of APH(3')-IIIa-mediated resistance to N1-substituted aminoglycoside antibiotics, Antimicrobial Agents and Chemotherapy 53, 3049-3055.

11. Mirza, I. A., Yachnin, B. J., Wang, S., Grosse, S., Bergeron, H., Imura, A., Iwaki, H., Hasegawa, Y., Lau, P. C. K., and Berghuis, A. M. (2009) Crystal Structures of Cyclohexanone Monooxygenase Reveal Complex Domain Movements and a Sliding Cofactor, J. Am. Chem. Soc. 131, 8848-8854.

12. Rodionov, D., Romero, P. A., Berghuis, A.M., Herscovics, A. (2009) Expression and purification of recombinant M-Pol I from Saccharomyces cerevisiae with alpha-1,6 mannosylpolymerase activity, Protein Expression and Purification 66, 1-6.

13. Xiong, B., Burk, D. L., Shen, J., Luo, X., Liu, H., Shen, J., Berghuis, A. M. (2008) The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation, Proteins 71, 1984-1994.

14. Miller, W. L., Matewish, M. J., McNally, D. J., Ishiyama, N., Anderson, E. M., Brewer, D., Brisson, J. R., Berghuis, A., and Lam, J. S. (2008) Flagellin glycosylation in Pseudomonas aeruginosa PAK requires the O-antigen biosynthesis enzyme WbpO, J Biol Chem 283, 3507-3518.

15. Peschard, P., Kozlov, G., Lin, T., Mirza, I. A., Berghuis, A., Lipkowitz, S., Park, M., and Gehring, K. (2007) Structural basis for ubiquitin-mediated dimerization and activation of the ubiquitin protein ligase Cbl-b, Molecular Cell 27, 474-485.

16. Korczynska, M., Mukhtar, T. A., Wright, G. D., and Berghuis, A. (2007) Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase, Proc Natl Acad Sci USA 104, 10388-10393.

17. Burk, D. L., Hwang, J., Kwok, E., Marrone, L., Goodfellow, V., Dmitrienko, G. I., and Berghuis, A. M. (2007) Structural studies of the final enzyme in the alpha-aminoadipate pathway-saccharopine dehydrogenase from Saccharomyces cerevisiae, Journal of Molecular Biology 373, 745-754.

18. Nascimento, M., Zhang, W. W., Ghosh, A., Houston, D. R., Berghuis, A., Olivier, M., and Matlashewski, G. (2006) Identification and characterization of a protein-tyrosine phosphatase in Leishmania: Involvement in virulence, J Biol Chem 281, 36257-36268.

19. Ishiyama, N., Creuzenet, C., Miller, W. L., Demendi, M., Anderson, E. M., Harauz, G., Lam, J. S., and Berghuis, A. (2006) Structural studies of FlaA1 from Helicobacter pylori reveal the mechanism for inverting 4,6-dehydratase activity, J Biol Chem 281, 24489-24495.

20. Gao, F., Yan, X., Shakya, T., Baettig, O., Ait-Mohand-Brunet, S., Berghuis, A., Wright, G. D., and Auclair, K. (2006) Synthesis and structure-activity relationships of truncated bisubstrate inhibitors of aminoglycoside 6'-N-acetyltransferases, J Med Chem 49, 5273-5281.

21. Fong, D., Yim, V. C., D'Elia, M. A., Brown, E. D., and Berghuis, A. (2006) Crystal structure of CTP:glycerol-3-phosphate cytidylyltransferase from Staphylococcus aureus: examination of structural basis for kinetic mechanism, Biochim Biophys Acta 1764, 63-69.

22. Mirza, I. A., Nazi, I., Korczynska, M., Wright, G. D., and Berghuis, A. (2005) Crystal structure of homoserine transacetylase from Haemophilus influenzae reveals a new family of alpha/beta-hydrolases, Biochemistry 44, 15768-15773.

23. Lemke, C., Hwang, J., Xiong, B., Cianciotto, N., and Berghuis, A. (2005) Crystallization and preliminary crystallographic analysis of an aminoglycoside kinase from Legionella pneumophila, Acta Crystallogr F Struct Biol Cryst Commun 61, 606-608.

24. Gao, F., Yan, X., Baettig, O., Berghuis, A., and Auclair, K. (2005) Regio- and chemoselective 6'-N-derivatization of aminoglycosides: bisubstrate inhibitors as probes to study aminoglycoside 6'-N-acetyltransferases, Angew Chem Int Ed Engl 44, 6859-6862.

25. Demendi, M., Ishiyama, N., Lam, J. S., Berghuis, A., and Creuzenet, C. (2005) Towards a better understanding of the substrate specificity of the UDP-N-acetylglucosamine C4 epimerase WbpP, Biochem J 389, 173-180.

26. Christensen, K. E., Mirza, I. A., Berghuis, A., and Mackenzie, R. E. (2005) Magnesium and phosphate ions enable NAD binding to methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase, J Biol Chem 280, 34316-34323.

27. Burk, D., Xiong, B., Breitbach, C., and Berghuis, A. (2005) Structures of aminoglycoside acetyltransferase AAC(6')-Ii in a novel crystal form: structural and normal-mode analyses, Acta Crystallogr D Biol Crystallogr 61, 1273-1279.

28. Bernatchez, S., Szymanski, C. M., Ishiyama, N., Li, J., Jarrell, H. C., Lau, P. C., Berghuis, A., Young, N. M., and Wakarchuk, W. W. (2005) A single bifunctional UDP-GlcNAc/Glc 4-epimerase supports the synthesis of three cell surface glycoconjugates in Campylobacter jejuni, J Biol Chem 280, 4792-4802.

29. Ishiyama, N., Creuzenet, C., Lam, J. S., and Berghuis, A. (2004) Crystal structure of WbpP, a genuine UDP-N-acetylglucosamine 4-epimerase from Pseudomonas aeruginosa: substrate specificity in udp-hexose 4-epimerases, J Biol Chem 279, 22635-22642.

30. Fong, D., and Berghuis, A. (2004) Crystallization and preliminary crystallographic analysis of 3′-aminoglycoside kinase type IIIa complexed with a eukaryotic protein kinase inhibitor, CKI-7, Acta Crystallogr D Biol Crystallogr 60, 1897-1899.

31. Ejim, L., Mirza, I. A., Capone, C., Nazi, I., Jenkins, S., Chee, G. L., Berghuis, A., and Wright, G. D. (2004) New phenolic inhibitors of yeast homoserine dehydrogenase, Bioorganic & Medicinal Chemistry 12, 3825-3830.

32. Jacques, S. L., Mirza, I. A., Ejim, L., Koteva, K., Hughes, D. W., Green, K., Kinach, R., Honek, J. F., Lai, H. K., Berghuis, A., and Wright, G. D. (2003) Enzyme-assisted suicide: molecular basis for the antifungal activity of 5-hydroxy-4-oxonorvaline by potent inhibition of homoserine dehydrogenase, Chemistry & Biology 10, 989-995.

33. Burk, D., Ghuman, N., Wybenga-Groot, L. E., and Berghuis, A. (2003) X-ray structure of the AAC(6')-Ii antibiotic resistance enzyme at 1.8 A resolution; examination of oligomeric arrangements in GNAT superfamily members, Protein Sci 12, 426-437.

34. Thompson, P. R., Boehr, D. D., Berghuis, A., and Wright, G. D. (2002) Mechanism of aminoglycoside antibiotic kinase APH(3')-IIIa: role of the nucleotide positioning loop, Biochemistry 41, 7001-7007.

35. Fong, D., and Berghuis, A. (2002) Substrate promiscuity of an aminoglycoside antibiotic resistance enzyme via target mimicry, EMBO J 21, 2323-2331.

36. Daigle, D. M., Rossi, L., Berghuis, A., Aravind, L., Koonin, E. V., and Brown, E. D. (2002) YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics, Biochemistry 41, 11109-11117.

37. Burk, D., and Berghuis, A. (2002) Protein kinase inhibitors and antibiotic resistance, Pharmacol Ther 93, 283-292.

38. Yim, V. C., Zolli, M., Badurina, D. S., Rossi, L., Brown, E. D., and Berghuis, A. M. (2001) Crystallization and preliminary X-ray diffraction studies of glycerol 3-phosphate cytidylyltransferase from Staphylococcus aureus, Acta Crystallogr D Biol Crystallogr 57, 918-920.

39. Leung, A. K., Duewel, H. S., Honek, J. F., and Berghuis, A. M. (2001) Crystal structure of the lytic transglycosylase from bacteriophage lambda in complex with hexa-N-acetylchitohexaose, Biochemistry 40, 5665-5673.

40. Burk, D. L., Hon, W. C., Leung, A. K., and Berghuis, A. M. (2001) Structural analyses of nucleotide binding to an aminoglycoside phosphotransferase, Biochemistry 40, 8756-8764.

41. DeLaBarre, B., Thompson, P. R., Wright, G. D., and Berghuis, A. M. (2000) Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases, Nat Struct Biol 7, 238-244.

42. Wybenga-Groot, L. E., Draker, K., Wright, G. D., and Berghuis, A. M. (1999) Crystal structure of an aminoglycoside 6'-N-acetyltransferase: defining the GCN5-related N-acetyltransferase superfamily fold, Structure 7, 497-507.

43. Thompson, P. R., Schwartzenhauer, J., Hughes, D. W., Berghuis, A. M., and Wright, G. D. (1999) The COOH terminus of aminoglycoside phosphotransferase (3')-IIIa is critical for antibiotic recognition and resistance, J Biol Chem 274, 30697-30706.

44. Wright, G. D., Berghuis, A. M., and Mobashery, S. (1998) Aminoglycoside antibiotics. Structures, functions, and resistance, Adv Exp Med Biol 456, 27-69.

45. DeLaBarre, B., Jacques, S. L., Pratt, C. E., Ruth, D. A., Wright, G. D., and Berghuis, A. M. (1998) Crystallization and preliminary X-ray diffraction studies of homoserine dehydrogenase from Saccharomyces cerevisiae, Acta Crystallogr D Biol Crystallogr 54, 413-415.

46. Hon, W. C., McKay, G. A., Thompson, P. R., Sweet, R. M., Yang, D. S., Wright, G. D., and Berghuis, A. M. (1997) Structure of an enzyme required for aminoglycoside antibiotic resistance reveals homology to eukaryotic protein kinases, Cell 89, 887-895.

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