Publications

Recent Articles | Articles (1997-2004) | Articles (1980-1996) | Review Articles | Editorial Material | Biographical Items | Notes

Recent Articles

Functional Characterization of cis and trans Activity of the Flavivirus NS2B-NS3 Protease. Aloke K. Bera, Richard J. Kuhn, Janet L. Smith. (2007) The Journal of Biological Chemistry, Vol. 282, Issue 16, 12883-12892.

Optical performance of the GM/CA CAT canted undulator beamlines for protein crystallography. R. F. Fischetti, S. Xu, D. Yoder, S. Stepanov, O. Makarov, R. Benn, S. Corcoran, W. Diete, M. Schwoerer-Bohning, R. Signorato, L. Schroeder, L. Berman, J. Viccaro, J. L. Smith. (2007) 9th International Conference on Synchrotron Radiation Instrumentation Amer. Inst. Phys. p. 754-757.

Functional Characterization of Cis and Trans Protease Activity of the Flavivirus NS2B-NS3 Protease. A. K. Bera, R. J. Kuhn and J. L. Smith. (2007) J. Biol. Chem. 2007 Mar 2; [Epub ahead of print]. Link

Tomar S., Hardy,R. W., Smith, J. L. and R. J. Kuhn. (2006) Catalytic core of alphavirus nonstructural protein nsP4 possesses terminal adenylyltransferase activity. J. Virology, 80, 9962-9969. PubMed Link

Sherman, D.H. and Smith, J.L. (2006) Clearing the skies over modular polyketide synthases. ACS Chem. Biol., 1, 505-509. PubMed Link

Akey, D.L., Kittendorf, J.D., Giraldes, J.W., Fecik, R.A., Sherman, D.H., Smith, J.L. (2006) Structural basis for macrolactonization by the pikromycin thioesterase. Nature Chemical Biology. 2, 537-542. PubMed Link

Giraldes, J.W., Akey, D.L., Kittendorf, J.D., Sherman, D.H., Smith, J.L., Fecik, R.A. (2006) Structural and mechanistic insights of polyketide macrolactonization from polyketide-based affinity labels. Nature Chemical Biology. 2, 531-536. PubMed Link

Cramer, W. A., Zhang, H. , Yan, J., Kurisu, G. and Smith, J. L. (2006) Trans-membrane traffic in the cytochrome b6f complex. Ann. Rev. Biochem. 75, 769-790.

Dahms, T. E. S., Sainz, G., Giroux, E. L., Caperelli, C. A., & Smith, J. L. (2005). The Apo and ternary complex structures of a chemotherapeutic target: Human glycinamide ribonucleotide transformylase. Biochemistry, 44, 9841-9850. PubMed Link

Chander, P., Halbig, K. M., Miller, J. K., Fields, C. J., Bonner, H. K. S., Grabner, G. K., Switzer, R. L., & Smith, J. L. (2005). Structure of the nucleotide complex of PyrR, the pyr attenuation protein from Bacillus caldolyticus, suggests dual regulation by pyrimidine and purine nucleotides. Journal of Bacteriology, 187, 1773-1782. PubMed Link

Zhu, J. H., Burgner, J. W., Harms, E., Belitsky, B. R., & Smith, J. L. (2005). A new arrangement of (beta/alpha)(8) barrels in the synthase subunit of PLP synthase. Journal of Biological Chemistry, 280, 27914-27923. PubMed Link

Wu, J. H., Bera, A. K., Kuhn, R. J., & Smith, J. L. (2005). Structure of the flavivirus helicase: Implications for catalytic activity, protein interactions, and proteolytic processing. Journal of Virology, 79, 10268-10277. PubMed Link

Cramer, W. A., Yan, J. S., Zhang, H. M., Kurisu, G., & Smith, J. L. (2005). Structure of the cytochrome b(6)f complex: New prosthetic groups, Q-space, and the "hors d'oeuvres hypothesis" for assembly of the complex. Photosynthesis Research, 85, 133-144. PubMed Link

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Articles (1997-2004)

Webster, T. J., Massa-Schlueter, E. A., Smith, J. L., & Slamovich, E. B. (2004). Osteoblast response to hydroxyapatite doped with divalent and trivalent cations. Biomaterials, 25, 2111-2121. PubMed Link

Sinha, S. C., Chaudhuri, B. N., Burgner, J. W., Yakovleva, G., Davisson, V. J., & Smith, J. L. (2004). Crystal structure of imidazole glycerol phosphate dehydratase - Duplication of an unusual fold. Journal of Biological Chemistry, 279, 15491-15498. PubMed Link

Choi, K. H., Groarke, J. M., Young, D. C., Kuhn, R. J., Smith, J. L., Pevear, D. C., & Rossmann, M. G. (2004). The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation. Proceedings of the National Academy of Sciences of the USA, 101, 4425-4430. PubMed Link

Choi, K. H., Groarke, J. M., Young, D. C., Rossmann, M. G., Pevear, D. C., Kuhn, R. J., & Smith, J. L. (2004). Design, expression, and purification of a Flaviviridae polymerase using a high-throughput approach to facilitate crystal structure determination. Protein Science, 13, 2685-2692. PubMed Link

Chaudhuri, B. N., Lange, S. C., Myers, R. S., Davisson, V. J., & Smith, J. L. (2003). Toward understanding the mechanism of the complex cyclization reaction catalyzed by imidazole glycerolphosphate synthase: Crystal structures of a ternary complex and the free enzyme. Biochemistry, 42, 7003-7012. PubMed Link

Myers, R. S., Jensen, J. R., Deras, I. L., Smith, J. L., & Davisson, V. J. (2003). Substrate-induced changes in the ammonia channel for imidazole glycerol phosphate synthase. Biochemistry, 42, 7013-7022. PubMed Link

Sinha, S. C., Krahn, J., Shin, B. S., Tomchick, D. R., Zalkin, H., & Smith, J. L. (2003). The purine repressor of Bacillus subtilis: A novel combination of domains adapted for transcription regulation. Journal of Bacteriology, 185, 4087-4098. PubMed Link

Bera, A. K., Zhu, J. H., Zalkin, H., & Smith, J. L. (2003). Functional dissection of the Bacillus subtilis pur operator site. Journal of Bacteriology, 185, 4099-4109. PubMed Link

Zhang, H. M., Kurisu, G., Smith, J. L., & Cramer, W. A. (2003). A defined protein-detergent-lipid complex for crystallization of integral membrane proteins: The cytochrome b(6)f complex of oxygenic photosynthesis. Proceedings of the National Academy of Sciences of the USA, 100, 5160-5163. PubMed Link

Kurisu, G., Zhang, H. M., Smith, J. L., & Cramer, W. A. (2003). Structure of the cytochrome b(6)f complex of oxygenic photosynthesis: Tuning the cavity. Science, 302, 1009-1014.

Sinha, S. C., & Smith, J. L. (2001). The PRT protein family. Current Opinion in Structural Biology, 11, 733-739. PubMed Link

Chaudhuri, B. N., Lange, S. C., Myers, R. S., Chittur, S. V., Davisson, V. J., & Smith, J. L. (2001). Crystal structure of imidazole glycerol phosphate synthase: A tunnel through a (beta/alpha)(8) barrel joins two active sites. Structure, 9, 987-997. PubMed Link

Ponamarev, M. V., Schlarb, B. G., Howe, C. J., Carrell, C. J., Smith, J. L., Bendall, D. S., & Cramer, W. A. (2000). Tryptophan-heme pi-electrostatic interactions in cytochrome f of oxygenic photosynthesis. Biochemistry, 39, 5971-5976. PubMed Link

Sainz, G., Carrell, C. J., Ponamarev, M. V., Soriano, G. M., Cramer, W. A., & Smith, J. L. (2000). Interruption of the internal water chain of cytochrome f impairs photosynthetic function. Biochemistry, 39, 9164-9173. PubMed Link

Bera, A. K., Chen, S., Smith, J. L., & Zalkin, H. (2000). Temperature-dependent function of the glutamine phosphoribosylpyrophosphate amidotransferase ammonia channel and coupling with glycinamide ribonucleotide synthetase in a hyperthermophile. Journal of Bacteriology, 182, 3734-3739. PubMed Link

Bera, A. K., Smith, J. L., & Zalkin, H. (2000). Dual role for the glutamine phosphoribosylpyrophosphate amidotransferase ammonia channel - Interdomain signaling and intermediate channeling. Journal of Biological Chemistry, 275, 7975-7979. PubMed Link

Carrell, C. J., Schlarb, B. G., Bendall, D. S., Howe, C. J., Cramer, W. A., & Smith, J. L. (1999). Structure of the soluble domain of cytochrome f from the cyanobacterium Phormidium laminosum. Biochemistry, 38, 9590-9599. PubMed Link

Chen, S. H., Burgner, J. W., Krahn, J. M., Smith, J. L., & Zalkin, H. (1999). Tryptophan fluorescence monitors multiple conformational changes required for glutamine phosphoribosylpyrophosphate amidotransferase interdomain signaling and catalysis. Biochemistry, 38, 11659-11669. PubMed Link

Li, S. T., Smith, J. L., & Zalkin, H. (1999). Mutational analysis of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase propeptide processing. Journal of Bacteriology, 181, 1403-1408. PubMed Link

Soriano, G. M., Ponamarev, M. V., Carrell, C. J., Xia, D., Smith, J. L., & Cramer, W. A. (1999). Comparison of the cytochrome bc(1) complex with the anticipated structure of the cytochrome b(6)f complex: De plus ca change de plus c'est la meme chose. Journal of Bioenergetics and Biomembranes, 31, 201-213. PubMed Link

Bera, A. K., Chen, S. H., Smith, J. L., & Zalkin, H. (1999). Interdomain signaling in glutamine phosphoribosylpyrophosphate amidotransferase. Journal of Biological Chemistry, 274, 36498-36504. PubMed Link

Smith, J. L. (1999). Forming and inhibiting PRT active sites. Nature Structural Biology, 6, 502-504. PubMed Link

Sinha, S., Rappu, P., Lange, S. C., Mantsala, P., Zalkin, H., & Smith, J. L. (1999). Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family. Proceedings of the National Academy of Sciences of the USA, 96, 13074-13079. PubMed Link

Smith, J. L. (1998). Glutamine PRPP amidotransferase: Snapshots of an enzyme in action. Current Opinion in Structural Biology, 8, 686-694. PubMed Link

Muchmore, C. R. A., Krahn, J. M., Kim, J. H., Zalkin, H., & Smith, J. L. (1998). Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Protein Science, 7, 39-51. PubMed Link

Tomchick, D. R., Turner, R. J., Switzer, R. L, & Smith, J. L. (1998). Adaptation of an enzyme to regulatory function: Structure of Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase. Structure, 6, 337-350. PubMed Link

Smith, J. L., & Thompson, A. (1998). Reactivity of selenomethionine - Dents in the magic bullet? Structure with Folding & Design, 6, 815-819. PubMed Link

Chen, S. H., Tomchick, D. R., Wolle, D., Hu, P., Smith, J. L., Switzer, R. L., & Zalkin, H. (1997). Mechanism of the synergistic end-product regulation of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase by nucleotides. Biochemistry, 36, 10718-10726. PubMed Link

Krahn, J. M., Kim, J. H., Burns, M. R., Parry, R. J., Zalkin, H., & Smith, J. L. (1997). Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site. Biochemistry, 36, 11061-11068. PubMed Link

Cramer, W. A., Soriano, G. M., Zhang, H. M., Ponamarey, M. V., & Smith, J. L. (1997). The cytochrome b(6)f complex. Novel aspects. Physiologia Plantarum, 100, 852-862.

Carrell, C. J., Zhang, H. M., Cramer, W. A., & Smith, J. L. (1997). Biological identity and diversity in photosynthesis and respiration: Structure of the lumen-side domain of the chloroplast Rieske protein. Structure, 5, 1613-1625. PubMed Link

Kim, J. H., Krahn, J. M., Tomchick, D. R., Smith, J. L., & Zalkin, H. (1996). Structure and function of the glutamine phosphoribosylpyrophosphate amidotransferase glutamine site and communication with the phosphoribosylpyrophosphate site. Journal of Biological Chemistry, 271, 15549-15557. PubMed Link

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Articles (1980-1996)

Zhang, J. M., Carrell, C. J., Huang, D. R., Sled, V., Ohnishi, T., Smith, J. L., & Cramer, W. A. (1996). Characterization and crystallization of the lumen side domain of the chloroplast Rieske iron-sulfur protein. Journal of Biological Chemistry, 271, 31360-31366. PubMed Link

Tesmer, J. G., Klem, T. J., Deras, M. L., Davisson, V. J., & Smith, J. L. (1996). The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. Nature Structural Biology, 3, 74-86. PubMed Link

Martinez, S. E., Huang, D., Ponomarev, M., Cramer, W. A., & Smith, J. L. (1996). The heme redox center of chloroplast cytochrome f is linked to a buried five-water chain. Protein Science, 5, 1081-1092.

Leesong, M., Henderson, B. S., Gillig, J. R., Schwab, J. M., & Smith, J. L. (1996). Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: Two catalytic activities in one active site. Structure, 4, 253-264. PubMed Link

Smith, J. L. (1995). Structures of glutamine amidotransferases from the purine biosynthetic pathway. Biochemical Society Transactions, 23, 894-898. PubMed Link

Smith, J. L. (1995). Enzymes of nucleotide synthesis. Current Opinion in Structural Biology, 5, 752-757. PubMed Link

Kim, J. H., Wolle, D., Haridas, K., Parry, R. J., Smith, J. L., & Zalkin, H. (1995). Stable carbocyclic analog of 5-phosphoribosyl-1-pyrophosphate to probe the mechanism of catalysis and regulation of glutamine phosphoribosylpyrophosphate amidotransferase. Journal of Biological Chemistry, 270, 17394-17399. PubMed Link

Brannigan, J. A., Dodson, G., Duggleby, H. J., Moody, P. C. E., Smith, J. L., Tomchick, D. R., & Murzin, A. G. (1995). A protein catalytic framework with an n-terminal nucleophile is capable of self-activation. Nature, 378, 416-419. PubMed Link

Cramer, W. A., Martinez, S. E., Huang, D., Tae, G. S., Everly, R. M., Heymann, J. B., Cheng, R. H., Baker, T. S., & Smith, J. L. (1994). Structural aspects of the cytochrome b(6)f complex - Structure of the lumen side domain of cytochrome f. Journal of Bioenergetics and Biomembranes, 26, 31-47. PubMed Link

Zhou, G. C., Smith, J. L., & Zalkin, H. (1994). Binding of purine nucleotides to two regulatory sites results in synergistic feedback inhibition of glutamine 5-phosphoribosylpyrophosphate amidotransferase. Journal of Biological Chemistry, 269, 6784-6789. PubMed Link

Tesmer, J. J. G., Stemmler, T. L., Penner-Hahn, J. E., Davisson, V. J., & Smith, J. L. (1994). Preliminary X-ray analysis of Escherichia coli GMP synthetase - Determination of anomalous scattering factors for a cysteinyl mercury derivative. Proteins: Structure, Function, and Genetics, 18, 394-403. PubMed Link

Smith, J. L., Zaluzec, E. J., Wery, J. P., Niu, L. W., Switzer, R. L., Zalkin, H., & Satow, Y. (1994). Structure of the allosteric regulatory enzyme of purine biosynthesis. Science, 264, 1427-1433. PubMed Link

Martinez, S. E., Huang, D., Szczepaniak, A., Cramer, W. A., & Smith, J. L. (1994). Crystal structure of chloroplast cytochrome f reveals a novel cytochrome fold and unexpected heme ligation. Structure, 2, 95-105. PubMed Link

Pahler, A., Smith, J. L., & Hendrickson, W. A. (1990). A probability representation for phase information from multi-wavelength anomalous dispersion. Acta Crystallographica, 46, 537-540.

Sharma, A., Henderson, B. S., Schwab, J. M., & Smith, J. L. (1990). Crystallization and preliminary X-ray analysis of beta-hydroxydecanoyl thiol ester dehydrase from Escherichia coli. Journal of Biological Chemistry, 265, 5110-5112. PubMed Link

Steczko, J., Muchmore, C. R., Smith, J. L., & Axelrod, B. (1990). Crystallization and preliminary X-ray investigation of lipoxygenase-1 from soybeans. Journal of Biological Chemistry, 265, 11352-11354. PubMed Link

Hendrickson, W. A., Pahler, A., Smith, J. L., Satow, Y., Merritt, E. A., & Phizackerley, R. P. (1989). Crystal structure of core streptavidin determined from multi-wavelength anomalous diffraction of synchrotron radiation. Proceedings of the National Academy of Sciences of the USA, 86, 2190-2194.

Smith, J. L., Corfield, P. W. R., Hendrickson, W. A., & Low, B. W. (1988). Refinement at 14A resolution of a model of erabutoxin B - Treatment of ordered solvent and discrete disorder. Acta Crystallographica, 44, 357-368.

Hendrickson, W. A., Smith, J. L., Phizackerley, R. P., & Merritt, E. A. (1988). Crystallographic structure analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. Proteins: Structure, Function, and Genetics, 4, 77-88. PubMed Link

Sheriff, S., Hendrickson, W. A., & Smith, J. L. (1987). Structure of myohemerythrin in the azidomet state at 1.7/1.3-A resolution. Journal of Molecular Biology, 197, 273-296.

Smith, J. L., Hendrickson, W. A., Honzatko, R. B., & Sheriff, S. (1986). Structural heterogeneity in protein crystals. Biochemistry, 25, 5018-5027. PubMed Link

Smith, J. L., & Sundaralingam, M. (1981). The structure of the antibiotic amicetin consisting of nucleobase, disaccharide and amino acid moieties. Acta Crystallographica, 37, 1095-1101.

Swaminathan, V., Smith, J. L., Sundaralingam, M., Coutsogeorgopoulos, C., & Kartha, G. (1981). Crystal and molecular structure of the antibiotic blasticidin S hydrochloride pentahydrate. Biochimica et Biophysica Acta, 655, 335-341. PubMed Link

Smith, J. L., Chwang, A., & Sundaralingam, M. (1980). The crystal structure and molecular conformation of 7,2'-anhydro-beta-d-arabinosylorotidine (cyclo ara-o). Acta Crystallographica, 36, 833-837.

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Review Articles

Cramer, W. A., Zhang, H., Yan, J., Kurisu, G. and Smith, J. L. (2006). Trans-membrane traffic in the cytochrome b6f complex. Annual Review of Biochemistry, 75, 769-790.

Smith, J. L., Zhang, H. M., Yan, J. S., Kurisu, G., & Cramer, W. A. (2004). Cytochrome bc complexes: A common core of structure and function surrounded by diversity in the outlying provinces. Current Opinion in Structural Biology, 14, 432-439.

Zalkin, H., & Smith, J. L. (1998). Enzymes utilizing glutamine as an amide donor. Advances in Enzymology, 72, 87-144.

Cramer, W. A., Soriano, G. M., Ponomarev, M., Huang, D., Zhang, H., Martinez, S. E., & Smith, J. L. (1996). Some new structural aspects and old controversies concerning the cytochrome b(6)f complex of oxygenic photosynthesis. Annual Review of Plant Physiology and Plant Molecular Biology, 47, 477-508.

Cramer, W. A., Martinez, S. E., Furbacher, P. N., Huang, D. & Smith, J. L. (1994). The cytochrome b(6)f complex. Current Opinion in Structural Biology, 4, 536-544.

Hendrickson, W. A., Smith, J. L., & Sheriff, S. (1985). Direct phase determination based on anomalous scattering. Methods in Enzymology, 115, 41-55.

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Editorial Material

Cramer, W. A., Zhang, H. M., Yan, J. S., Kurisu, G., & Smith, J. L. (2004). Evolution of photosynthesis: Time-independent structure of the cytochrome b(6)f complex. Biochemistry, 43, 5921-5929.

Kuller, A., Fleri, W., Bluhm, W. F., Smith, J. L., Westbrook, J., & Bourne, P. E. (2002). A biologist's guide to synchrotron facilities: The BioSync web resource. Trends in Biochemical Sciences, 27, 213-215.

Deisenhofer, J., & Smith, J. L. (2001). Proteins - Editorial overview. Current Opinion in Structural Biology, 11, 701-702.

Kuller, A., Fleri, W., Bluhm, W. F., Bourne, P. E., Smith, J. L., & Westbrook, J. (2001). Announcement of the BioSync web site. Nature Structural Biology, 8, 663.

Smith, J. L., & Wright, P. (1998). Biophysical methods - Advances in biophysical methods: The whole is greater than the sum of the parts. Current Opinion in Structural Biology, 8, 593-594.

Smith, J. L. (1998). Structural biology - Secret life of cytochrome bc(1). Science, 281, 58-59.

Wright, P., & Smith, J. L. (1996). Biophysical methods faster and bigger - Editorial overview. Current Opinion in Structural Biology, 6, 583-584.

Smith, J. L., & Wright, P. (1993). Biophysical methods - Editorial overview. Current Opinion in Structural Biology, 3, 723-724.

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Biographical Item

Smith, J. L. (2004). Carl-Ivar Branden (1934-2004) - Obituary. Acta Crystallographica, 60, 1509-1511.

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Notes

Martinez, S. E., & Smith, J. L. (1991). Crystallization and preliminary characterization of mitogillin, a ribosomal ribonuclease from Aspergillus restrictus. Journal of Molecular Biology, 218, 489-492.

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