Researcher Profiles

Return to member profile

Stephen K. Burley, MD, DPhil

Publications since 2011

Adams, P. D. Aertgeerts, K. Bauer, C. Bell, J. A. Berman, H. M. Bhat, T. N. Blaney, J. M. Bolton, E. Bricogne, G. Brown, D. Burley, S. K. Case, D. A. Clark, K. L. Darden, T. Emsley, P. Feher, V. A. Feng, Z. Groom, C. R. Harris, S. F. Hendle, J. Holder, T. Joachimiak, A. Kleywegt, G. J. Krojer, T. Marcotrigiano, J. Mark, A. E. Markley, J. L. Miller, M. Minor, W. Montelione, G. T. Murshudov, G. Nakagawa, A. Nakamura, H. Nicholls, A. Nicklaus, M. Nolte, R. T. Padyana, A. K. Peishoff, C. E. Pieniazek, S. Read, R. J. Shao, C. Sheriff, S. Smart, O. Soisson, S. Spurlino, J. Stouch, T. Svobodova, R. Tempel, W. Terwilliger, T. C. Tronrud, D. Velankar, S. Ward, S. C. Warren, G. L. Westbrook, J. D. Williams, P. Yang, H. Young, J. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure, 24:502-508, . (PMID: 27050687)

Sali, A. Berman, H. M. Schwede, T. Trewhella, J. Kleywegt, G. Burley, S. K. Markley, J. Nakamura, H. Adams, P. Bonvin, A. M. Chiu, W. Peraro, M. D. Di Maio, F. Ferrin, T. E. Grunewald, K. Gutmanas, A. Henderson, R. Hummer, G. Iwasaki, K. Johnson, G. Lawson, C. L. Meiler, J. Marti-Renom, M. A. Montelione, G. T. Nilges, M. Nussinov, R. Patwardhan, A. Rappsilber, J. Read, R. J. Saibil, H. Schroder, G. F. Schwieters, C. D. Seidel, C. A. Svergun, D. Topf, M. Ulrich, E. L. Velankar, S. Westbrook, J. D. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure, In process, . (PMID: 26095030)

Goodsell, D. S. Dutta, S. Zardecki, C. Voigt, M. Berman, H. M. Burley, S. K. The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology. PLoS Biol, 13:e1002140, . (PMID: 25942442)

Wu, T. J. Wang, X. Zhang, Y. Meng, L. Kerrigan, J. E. Burley, S. K. Zheng, X. F. Identification of a Non-Gatekeeper Hot Spot for Drug-Resistant Mutations in mTOR Kinase. Cell Rep, In process, . (PMID: 25865887)

Rose, P. W. Prlic, A. Bi, C. Bluhm, W. F. Christie, C. H. Dutta, S. Green, R. K. Goodsell, D. S. Westbrook, J. D. Woo, J. Young, J. Zardecki, C. Berman, H. M. Bourne, P. E. Burley, S. K. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res, In process, . (PMID: 25428375)

Kim, S. J. Fernandez-Martinez, J. Sampathkumar, P. Martel, A. Matsui, T. Tsuruta, H. Weiss, T. Markina-Inarrairaegui, A. Bonanno, J. B. Sauder, J. M. Burley, S. K. Almo, S. C. Rout, M. Sali, A. Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex. Mol Cell Proteomics, 13:2911-2926, . (PMID: 25139911, PMCID: PMC4223481)

Berman, H. M. Burley, S. K. Kleywegt, G. J. Nakamura, H. Markley, J. L. Response to On prompt update of literature references in the Protein Data Bank. Acta Crystallogr D Biol Crystallogr, 70:2780, . (PMID: 25286863)

Manjasetty, B. A. Chance, M. R. Burley, S. K. Panjikar, S. Almo, S. C. Crystal structure of Aspartate kinase (AK): An important allosteric enzyme for amino acids production. Biotechnol Rep (Amst), 3:73-85, . (PMID: 25170437, PMCID: PMC4142519)

Korczynska, M. Xiang, D. F. Zhang, Z. Xu, C. Narindoshvili, T. Kamat, S. S. Williams, H. J. Chang, S. S. Kolb, P. Hillerich, B. Sauder, J. M. Burley, S. K. Almo, S. C. Swaminathan, S. Shoichet, B. K. Raushel, F. M. Functional Annotation and Structural Characterization of a Novel Lactonase Hydrolyzing d-Xylono-1,4-lactone-5-phosphate and l-Arabino-1,4-lactone-5-phosphate. Biochemistry, 53:4727-4738, . (PMID: 24955762, PMCID: PMC4108184)

Odokonyero, D. Sakai, A. Patskovsky, Y. Malashkevich, V. N. Fedorov, A. A. Bonanno, J. B. Fedorov, E. V. Toro, R. Agarwal, R. Wang, C. Ozerova, N. D. Yew, W. S. Sauder, J. M. Swaminathan, S. Burley, S. K. Almo, S. C. Glasner, M. E. Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family. Proc Natl Acad Sci U S A, 111:8535-8540, . (PMID: 24872444, PMCID: PMC4060685)

Goodsell, D. S. Burley, S. K. Berman, H. M. Revealing structural views of biology. Biopolymers, 99:817-824, . (PMID: 23821527)

Odokonyero, D. Ragumani, S. Swaminathan, S. Lopez, M. S. Bonanno, J. B. Ozerova, N. D. Woodard, D. R. Machala, B. W. Burley, S. K. Almo, S. C. Glasner, M. E. Divergent Evolution of Ligand Binding in the o-Succinylbenzoate Synthase Family. Biochemistry, 52:7512-7521, . (PMID: 24060347, PMCID: PMC3908897)

Daughtry, K. D. Huang, H. Malashkevich, V. Patskovsky, Y. Liu, W. Ramagopal, U. Sauder, J. M. Burley, S. K. Almo, S. C. Dunaway-Mariano, D. Allen, K. N. Structural Basis for the Divergence of Substrate Specificity and Biological Function within HAD Phosphatases in Lipopolysaccharide and Sialic Acid Biosynthesis. Biochemistry, 52:5372-5386, . (PMID: 23848398)

Almo, S. C. Garforth, S. J. Hillerich, B. S. Love, J. D. Seidel, R. D. Burley, S. K. Protein production from the structural genomics perspective: achievements and future needs. Curr Opin Struct Biol, 23:335-344, . (PMID: 23642905)

Sampathkumar, P. Kim, S. J. Upla, P. Rice, W. J. Phillips, J. Timney, B. L. Pieper, U. Bonanno, J. B. Fernandez-Martinez, J. Hakhverdyan, Z. Ketaren, N. E. Matsui, T. Weiss, T. M. Stokes, D. L. Sauder, J. M. Burley, S. K. Sali, A. Rout, M. P. Almo, S. C. Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. Structure, 21:560-571, . (PMID: 23499021, PMCID: PMC3755625)

Burley, S. K. PDB40: The Protein Data Bank celebrates its 40th birthday. Biopolymers, 99:165-169, . (PMID: 23280389)

Palani, K. Burley, S. K. Swaminathan, S. Structure of alanine racemase from Oenococcus oeni with bound pyridoxal 5'-phosphate. Acta Crystallogr Sect F Struct Biol Cryst Commun, 69:15-19, . (PMID: 23295479, PMCID: PMC3539696)

Knapp, S. Arruda, P. Blagg, J. Burley, S. Drewry, D. H. Edwards, A. Fabbro, D. Gillespie, P. Gray, N. S. Kuster, B. Lackey, K. E. Mazzafera, P. Tomkinson, N. C. Willson, T. M. Workman, P. Zuercher, W. J. A public-private partnership to unlock the untargeted kinome. Nat Chem Biol, 9:3-6, . (PMID: 23238671)

Palani, K. Kumaran, D. Burley, S. K. Swaminathan, S. Structure of a periplasmic glucose-binding protein from Thermotoga maritima. Acta Crystallogr Sect F Struct Biol Cryst Commun, 68:1460-1464, . (PMID: 23192024, PMCID: PMC3509965)

Garside, E. L. Schellenberg, M. J. Gesner, E. M. Bonanno, J. B. Sauder, J. M. Burley, S. K. Almo, S. C. Mehta, G. MacMillan, A. M. Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases. RNA, 18:2020-2028, . (PMID: 23006625, PMCID: PMC3479392)

Warlick, B. P. Evans, B. S. Erb, T. J. Ramagopal, U. A. Sriram, J. Imker, H. J. Sauder, J. M. Bonanno, J. B. Burley, S. K. Tabita, F. R. Almo, S. C. Sweedler, J. S. Gerlt, J. A. 1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum. Biochemistry, 51:8324-8326, . (PMID: 23035785, PMCID: PMC3490199)

Sampathkumar, P. Kim, S. J. Manglicmot, D. Bain, K. T. Gilmore, J. Gheyi, T. Phillips, J. Pieper, U. Fernandez-Martinez, J. Franke, J. D. Matsui, T. Tsuruta, H. Atwell, S. Thompson, D. A. Emtage, J. S. Wasserman, S. R. Rout, M. P. Sali, A. Sauder, J. M. Almo, S. C. Burley, S. K. Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata. Proteins, 80:2110-2116, . (PMID: 22544723, PMCID: PMC3686472)

Wasserman, S. R. Koss, J. W. Sojitra, S. T. Morisco, L. L. Burley, S. K. Rapid-access, high-throughput synchrotron crystallography for drug discovery. Trends Pharmacol Sci, 33:261-267, . (PMID: 22521107)

Hobbs, M. E. Malashkevich, V. Williams, H. J. Xu, C. Sauder, J. M. Burley, S. K. Almo, S. C. Raushel, F. M. Structure and catalytic mechanism of LigI: insight into the amidohydrolase enzymes of cog3618 and lignin degradation. Biochemistry, 51:3497-3507, . (PMID: 22475079, PMCID: PMC3416963)

Agarwal, R. Burley, S. K. Swaminathan, S. Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase. Proteins, 80:261-268, . (PMID: 22072612, PMCID: PMC3240725)

Kamat, S. S. Holmes-Hampton, G. P. Bagaria, A. Kumaran, D. Tichy, S. E. Gheyi, T. Zheng, X. Bain, K. Groshong, C. Emtage, S. Sauder, J. M. Burley, S. K. Swaminathan, S. Lindahl, P. A. Raushel, F. M. The catalase activity of diiron adenine deaminase. Protein Sci, 20:2080-2094, . (PMID: 21998098, PMCID: PMC3302651)

Suttisansanee, U. Lau, K. Lagishetty, S. Rao, K. N. Swaminathan, S. Sauder, J. M. Burley, S. K. Honek, J. F. Structural variation in bacterial glyoxalase I enzymes: investigation of the metalloenzyme glyoxalase I from Clostridium acetobutylicum. J Biol Chem, 286:38367-38374, . (PMID: 21914803, PMCID: PMC3207458)

Goble, A. M. Zhang, Z. Sauder, J. M. Burley, S. K. Swaminathan, S. Raushel, F. M. Pa0148 from Pseudomonas aeruginosa catalyzes the deamination of adenine. Biochemistry, 50:6589-6597, . (PMID: 21710971, PMCID: PMC3151671)

Burley, S. K. Sonenberg, N. Gimme phospho-serine five! Capping enzyme guanylyltransferase recognition of the RNA polymerase II CTD. Mol Cell, 43:163-165, . (PMID: 21777807)

Teplova, M. Malinina, L. Darnell, J. C. Song, J. Lu, M. Abagyan, R. Musunuru, K. Teplov, A. Burley, S. K. Darnell, R. B. Patel, D. J. Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1. Structure, 19:930-944, . (PMID: 21742260, PMCID: PMC3134789)

Shi, W. Punta, M. Bohon, J. Sauder, J. M. D'Mello, R. Sullivan, M. Toomey, J. Abel, D. Lippi, M. Passerini, A. Frasconi, P. Burley, S. K. Rost, B. Chance, M. R. Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy. Genome Res, 21:898-907, . (PMID: 21482623, PMCID: PMC3106322)

Sampathkumar, P. Gheyi, T. Miller, S. A. Bain, K. T. Dickey, M. Bonanno, J. B. Kim, S. J. Phillips, J. Pieper, U. Fernandez-Martinez, J. Franke, J. D. Martel, A. Tsuruta, H. Atwell, S. Thompson, D. A. Emtage, J. S. Wasserman, S. R. Rout, M. P. Sali, A. Sauder, J. M. Burley, S. K. Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex. Proteins, 79:1672-1677, . (PMID: 21365675, PMCID: PMC3350809)

Bagaria, A. Kumaran, D. Burley, S. K. Swaminathan, S. Structural basis for a ribofuranosyl binding protein: insights into the furanose specific transport. Proteins, 79:1352-1357, . (PMID: 21387413, PMCID: PMC3077950)

Kamat, S. S. Bagaria, A. Kumaran, D. Holmes-Hampton, G. P. Fan, H. Sali, A. Sauder, J. M. Burley, S. K. Lindahl, P. A. Swaminathan, S. Raushel, F. M. Catalytic mechanism and three-dimensional structure of adenine deaminase. Biochemistry, 50:1917-1927, . (PMID: 21247091, PMCID: PMC3059353)

Kamat, S. S. Fan, H. Sauder, J. M. Burley, S. K. Shoichet, B. K. Sali, A. Raushel, F. M. Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc, 133:2080-2083, . (PMID: 21275375, PMCID: PMC3043370)

Zhang, Z. Zhou, R. Sauder, J. M. Tonge, P. J. Burley, S. K. Swaminathan, S. Structural and functional studies of fatty acyl adenylate ligases from E. coli and L. pneumophila. J Mol Biol, 406:313-324, . (PMID: 21185305, PMCID: PMC3040979)

Pieper, U. Webb, B. M. Barkan, D. T. Schneidman-Duhovny, D. Schlessinger, A. Braberg, H. Yang, Z. Meng, E. C. Pettersen, E. F. Huang, C. C. Datta, R. S. Sampathkumar, P. Madhusudhan, M. S. Sjolander, K. Ferrin, T. E. Burley, S. K. Sali, A. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res, 39:D465-D474, . (PMID: 21097780, PMCID: PMC3013688)