Publications

    2020
  1. Dong, S.H., Cogan, D.P., and Nair, S.K. (2020) “Structural Biology of RiPP Natural Products Biosynthesis.” Comprehensive Natural Products III: Chemistry and Biology, doi:10.1016/B978-0-12-409547-2.14686-4.
  1. Kapoor, I., Olivares, P., and Nair, S.K. (2020) “Biochemical basis for the regulation of biosynthesis of antiparasitics by bacterial hormones.” eLife, doi:10.7554/eLife.57824.
  1. Bogart, J.W., Kramer, N.J., Turlik, A., Bleich, R.M., Catlin, D.S., Schroeder, F.C., Nair, S.K., Williamson, R.T., Houk, K.N., and Bowers, A.A. (2020) “Interception of the Bycroft-Gowland intermediate in the Enzymatic Macrocyclization of Thiopeptides.” J. Am. Chem. Soc., doi:10.1021/jacs.0c05639.
  1. Dong, S.H., Nhu-Lam, M., Nagarajan, R., and Nair, S.K. (2020) “Structure-guided biochemical analysis of quorum signal synthase specificities.” ACS Chem Biology, doi:10.1021/acschembio.0c00142.
  1. Nayak, D.D., Liu, A., Agrawak, N., Rodriguez-Carerro, R., Dong, S.H., Mitchell, D.A., Nair, S.K., and Metcalf, W.W. (2020) “Functional interactions between posttranslationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans.” PloS Biology 18, e30000507.
  1. Nair, S.K., and Jez, J.M. (2020) “Natural product biosynthesis: What’s next? An introduction to the JBC reviews thematic series.” J. Biol. Chem 295, 335-6.
  1. Huo, L., Zhao, X., Acedo, J.Z., Estrada, P., Nair, S.K., and van der Donk, W.A. (2020) “Characterization of a dehydratase and methyltransferase in the biosynthesis of ribosomal synthesized and post-translationally modified peptides in Lachnospiraceae.” Chembiochem 21, 190-99.
    2019
  1. Chekan, J., Ongpipattanakul, C., and Nair, S.K. (2019) “Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis.” Proc. Natl. Acad. Sci. 116, 24049-55.
  1. Bothwell, I.R., Cogan, D.P., Kim, T., Reinhardt, C.J., van der Donk, W.A.(*), and Nair, S.K.(*) (2019) “Characterization of glutamyl-tRNA-dependent dehydratases using nonreactive substrate mimics.” Proc. Natl. Acad. Sci. 116, 17245-250.
  1. Chekan, J., Ongpipattanakul, C., Wright, T.R., Zhang, B., Bollinger, J.M., Rajakovich, L.J., Crebs, C.M., Cicchillo, R.M., and Nair, S.K. (2019) “Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants.” Proc. Natl. Acad. Sci. 116, 13299-304.
  1. Dong, S., Liu, A., Mahanta, N., Mitchell, D.A.* and Nair, S.K.* (2019) “Mechanistic basis for ribosomal peptide backbone modifications.” ACS Cent. Sci. 22, 842-51. (*Corresponding author)
  1. Dong, S., Kulikovsky, A., Zukher, I., Estrada, P., Dubiley, S., Severinov, K.* and Nair, S.K.* (2019) “Biosynthesis of the RiPP Trojan horse nucleotide antibiotic microcin C is directed by the N-formyl of the peptide precursor” Chem. Sci. 10, 2391-95. (*Corresponding author)
  1. Petronikolou, N., Ortega, M., Borisova, S., Nair, S.K.* and Metcalf, W.W.* (2019) “Molecular basis of Bacillus subtitles ATCC6623 self-resistance to the phosphono-oligopeptide antibiotic rhizocticin” ACS Chem. Bio. 14, 742-50. (*Corresponding author)
  1. Nguyen, K., DeSieno, M.A., Bae, B., Johanes, T.W., Cobb, R.E., Zhao, H.* and Nair, S.K.* (2019) “ICharacterization of the flavin monooxygenase involved in the biosynthesis of the antimalarial FR-9000098″ Org. Biomol. Chem. 17, 1506-18. (*Corresponding author)
  1. Bobeica, S.C., Dong, S., Huo, L., Mazo, N., McLaughlin, M.H., Jimenez-Oses, G., Nair, S.K.*, and van der Donk, W.A.* (2019) “Insights into AMS/PCAT transporters from biochemical and structural characterization of a double Glycine motif protease” eLife doi: 10.755/eLife.42305. (*Corresponding author)
    2018
  1. Estrada, P., Morita, M., Hao, Y., Schmidt, E.W.*, and Nair, S.K.*  (2018) “A Single Amino Acid Switch Alters the Isoprene Donor Specificity in RiPP Prenyltransferases” J. Am. Chem. Soc. 140, 8124-27. (*Corresponding author)
  1. Ongpipattanakul, C., and Nair, S.K. (2018) “Molecular Basis for Autocatalytic Backbone N-Methyltation in RiPP Natural Product Biosynthesis” ACS Chem. Bio. 13, 2989-99.
  1. An, L., Cogan, D.P., Navo, C.D., Jimenez-Uses, G., Nair, S.K.*, and van der Donk, W.A.*  (2018) “Substrate-assisted Enzymatic Formation of Lysinoalanine in Duramycin” Nature Chem. Bio. 14, 928-33. (*Corresponding author)
  1. Kapoor, I., and Nair, S.K. (2018) “Structure-Guided Analyses of a Key Enzyme Involved in the Biosynthesis of an Antivitamin” Biochemistry 57, 5282-88.
  1. O’Reilly, M.C., Dong, S.H., Rossi, F.M., Karlen, K.M., Kumar, R.S., Nair, S.K.*, and Blackwell, H.E.*  (2018) “Structural and Biochemical Studies of Non-native Agonists of the LasR Quorum-Sensing Receptor Reveal an L3 Loop “Out” Conformation for LasR” Cell Chem. Biol. 25, 1128-39. (*Corresponding author)
  1. Cogan, D.P., Baraquet, C., Harwood, C., and Nair, S.K.  (2018) “Structural basis of transcriptional regulation by CouR, a repressor of coumarate catabolism in Rhodopseudomonas palustris” J. Biol. Chem. 293, 11727-735.
  1. Petronikolou, N. and Nair, S.K.  (2018) “Structural and Biochemical Studies of a Biocatalyst for the Enzymatic Production of Wax Esters” ACS Catalysis 8, 6334-44.
  1. Gu, W., Dong, S.H., Sarkar, S., Nair, S.K.*, and Schmidt, E.W.*  (2018) “The Biochemistry and Structural Biology of Cyanobactin Pathways: Enabling Combinatorial Biosynthesis.” Methods Enzymol. 604, 113-63. (*Corresponding author)
  1. Morita, M., Hao, Y., Jokela, J.K., Sardar, D., Lin, Z., Sivonen, K. Nair, S.K.*, and Schmidt, E.W.*  (2018) “Post-translational Tyrosine Geranylation in Cyanobactin Biosynthesis.” J. Am. Chem. Soc. 140, 6044-48. (*Corresponding author)
  1. Ongpipattanakul, C.,and Nair, S.K. (2018) “Perspectives: Biosynthetic Proteases that Catalyze the Macrocyclization of Ribosomally Synthesized Linear Peptides.” Biochemistry 57, 3201-09.
  1. Mahanta, N., Liu, A., Dong, S.H., Nair, S.K., and Mitchell, D.A. (2018) “Enzymatic reconstitution of ribosomal peptide backbone thioamidation.” Proc. Natl. Acad. Sci. 115, 3030-35.
  1. Petronikolou, N., Hollatz, A.J., Schuler, M.A., and Nair, S.K. (2018) “Loganic Acid Methyltransferase: Insights into the Specificity of Methylation on an iridoid Glycoside.” Chembiochem 19, 784-88.
    2017
  1. Cogan, D.P., Hudson, G.A., Zhang, G., Pogorelov, T.V., van der Donk, W.A., Mitchell, D.A. and Nair, S.K. (2017) “Structural insights into enzymatic [4+2] aza-cycloaddition in thiopeptide antibiotic biosynthesis.” Proc. Natl. Acad. Sci. 114, 12928-33.
  1. Dong, S.H., Frane, N.D., Christensen, Q.H., Greenberg, E.P., Nagarajan, R., and Nair, S.K. (2017) “Molecular basis for the substrate specificity of quorum signal synthases.” Proc. Natl. Acad. Sci. 114, 9092-97.
  1. Chekan, J.R., Estrada, P., Covello, P.S., and Nair, S.K. (2017) “Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants.” Proc. Natl. Acad. Sci. 114, 6551-56.
  1. Estrada, P., Manandhar, M., Dong, S.H., Deveryshetty, J., Agarwal, V., Cronan, J.E., and Nair, S.K. (2017) “Structure and function of the pimeloyl-CoA synthetase BioW defines a new fold for adenylate-forming enzymes.” Nature Chem. Bio. 13, 668-74.
  1. Repka, L.M., Chekan, J.R., Nair, S.K.*, and van der Donk, W.A.* (2017) “Mechanistic Understandingof Lanthipeptide Biosynthetic Enzymes.” Chemical Reviews 117, 5457-5520.  (*Corresponding author)
  1. Sardar, D., Hao, Y., Morita, M., Nair, S.K.*, and Schmidt, E.W.* (2017) “Enzymatic N- and C-Protecion in Cyanobactin RiPP Natural Products.” J. Am. Chem. Soc. 139, 2884-87. (*Corresponding author)
  1. Ortega, M.A., Cogan, D.P., Mukherjee, S., Garg, N., Li, B., Thibodeaux, G.N., Maffioli, S.I., Donadio, S., Sosio, M., Escano, J., Smith, L., Nair, S.K.*, and van der Donk, W.A. (2017) “Two Flavoenzymes Catalyze the Post-translational Generation of 5-Chlorotryptophan and Aminovinyl-Cysteine During NAI-107 Biosynthesis.” ACS Chem. Bio. 12, 548-557. (*Corresponding author)
  1. Olivares, P., Ulrich, E.C., Chekan, J.R., van der Donk, W.A.*, and Nair, S.K.* (2017) “Characterization of Two Late-Stage Enzymes Involved in Fosfomycin Biosynthesis in Pseudomonads.” ACS Chem. Bio. 12, 456-63. (*Corresponding author)
    2016
  1. Chekan, J.R., Koos, J.D., Zong, C., Maksimov, M.O., Link, A.J., and Nair, S.K. (2016) “Structure of the Lasso Peptide Isopeptidase Identifies a Topology for Processing Threaded Substrates.” J. Am. Chem. Soc. 138, 16452-58.
  1. Hao, Y., Pierce, E., Roe, D.R., McIntosh, J., Agarwal, V., Cheatham, T.E., Schmidt, E.W.*, and Nair, S.K.* (2016) “Molecular basis for the broad selectivity of a peptide prenyltransferase.” Proc. Nat’l Acad. Sci. USA113, 14037-42.
  1. Chekan, J.R., Cogan, D.P., and Nair, S.K. (2016) “Molecular Basis for Resistance Against Phosphonate Antibiotics and Herbicides.” MedChemComm 7, 28-36.
  1. Ortega, M.A., Hao, Y., Walker, M.C., Donadio, S., Sosio, M., Nair, S.K.* and van der Donk, W.A.* (2016) “Structure and tRNA Specificity of MibB, a Lantibiotic Dehydratase from Actinobacteria Involved in NAI-107 Biosynthesis.” Cell Chem. Bio. 23, 370-80 (*Corresponding author)
    2015
  1. Petronikolou, N., and Nair, S.K. (2015) “Biochemical Studies of Mycobacterial Fatty Acid Methyltransferase: A Catalysts for the Enzymatic Production of Biodiesel.” Chem. Bio. 19, 1480-90.
  1. Tang, W., Dong, S.H., Repka, L., He, C., Nair, S.K.*, and van der Donk, W.A.* (2015) “Class II lanthipeptides harbor a pool of sequence-specific LanP proteases.” Chem. Sci. 6, 6270-79. (*Corresponding author)
  1. Li, Z., and Nair, S.K. (2015) “Structural Bases for Specificity and Flexibility in a Plant 4-Coumarate:CoA Ligase.” Structure 23, 2032-42.
  1. Dong, S.H., Tang, W., Lukk, T., Yu, Y., Nair, S.K.*, and van der Donk, W.A.* (2015) “The enterrococcal cytolysin synthetase has an unanticipated lipid kinase fold.” eLife 10, 07607. (*Corresponding author)
  1. Ortega, M., Hao, Y., Zhang, Q., Walker, M.C., van der Donk, W.A.*, and Nair, S.K.* (2015) “Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB.” Nature 527, 509-12. (*Corresponding author) [Highlighted in Chemical & Engineering News, etc.].
  1. Hao, Y., Blair, P., Sharma, A., Mitchell, D.A.*, and Nair, S.K.* (2015) “Insights into methyltransferase specificity and bioactivity of derivatives of the antibiotic plantazolicin.” ACS Chem. Bio. 15, 1209-16. (*Corresponding author)
  1. Garg, A., Lukk, T., Kumar, V., Choi, J.Y., Augagneur, Y., Voelkerm D.R., Nair, S.K., and Ben Mamoun, C. (2015) “Structure, function and inhibition of the phosphoethanolamine methyltransferases of the human malaria parasites Plasmodium vivax and Plasmodium knowlesi.” Sci. Rep. 5, 9064.
  1. Peck, S.C., Chekan, J.R., Ulrich, E.C., Nair, S.K., and van der Donk, W.A. (2015) “A common late-stage intermediate in catalysis by 2-hydroxyethyl-phosphonate dioxygenase and methylphosphonate synthase.” J. Am. Chem. Soc. 137, 3217-20.
  1. Cobb, R.E., Bae, B., Li, Z., DeSieno, M.A., Nair, S.K., and Zhao, H. (2015) “Structure-guided design and biosynthesis of a novel FR-900098 analogue as a potent Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr) inhibitor.” Chem. Comm. 51, 2526-28.
  1. Zhang, M., Chekan, J.R., Dodd, D., Hong, P.Y., Radlinski, L., Revindran, V., Nair, S.K.*, Mackie R.I.*, and Cann I.* (2015) “Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes.” Proc. Nat’l Acad. Sci USA. 111, E3708-17. (*Corresponding author) [Highlighted in Chemical & Engineering News].
    2014
  1. Van der Donk, W.A.*, and Nair, S.K.* (2014) “Structure and mechanism of lanthipeptide biosynthetic enzymes.” Curr. Opin. Struct. Biol. 29, 58-66. (*Corresponding author)
  1. Chekan, J.R., Kwon, I.H., Agarwal, V., Dodd, D., Revindran, V., Mackie, R.I., Cann, I., and Nair, S.K. (2014) “Structure and biochemical basis for mannan utilization by Caldanaerobius polysaccharolyticus strain ATCC BAA-17.” J. Biol. Chem. 289, 34965-77.
  1. Dunbar, K.L., Chekan, J.R., Cox, C.L., Burkhart, B.J., Nair, S.K.* and Mitchell, D.A.* (2014) “Discovery of a new ATP-binding motif involved in peptide azoline biosynthesis.” Nature Chem. Bio. 10, 823-29. (*Corresponding author)
  1. Ortega, M.A., Velazquez, J.E., Garg, N., Zhang, Q., Joyce, C.E., Nair, S.K.* and van der Donk, W.A.* (2014) “Substrate specificity of the lanthipeptide peptidase ElxP and the oxidoreductase ElxO.” ACS Chem. Bio. 9, 1718-25. (*Corresponding author)
  1. Agarwal, V. Vondenhoff, G., Gadakh, B., Severinov, K., van Aershot, A., and Nair, S.K. (2014) “Exploring the substrate promiscuity of an antibiotic inactivating enzyme.” MedChemComm 5, 1567-70.
  1. Majumdar, S., Lukk, T., Solbiati, J., Bauer, S., Nair, S.K., Cronan, J.E., and Gerlt, J.A. (2014) “The roles of small laccases from Streptomyces in lignin degradation.” Biochemistry, 53, 4047-58.
  1. Hung, J.E., Fogle, E.J., Garg, N., Chekan, J.R., Nair, S.K., and van der Donk, W.A. (2014) “Chemical rescues and inhibition studies to determine the role of Arg301 in phosphite dehydrogenase.” PloS One 9: e87134.
  1. Agarwal, V. Peck, S.C., Chen, J.H., Borisova, S.A., Chekan, J.R., van der Donk, W.A.*, and Nair, S.K.* (2014) “Structure and function of phosphonoacetaldehyde dehydrogenase: the missing link in phosphonoacetate formation.” Chem. Bio. 16, 125-135. (*Corresponding author)
  1. Park. D. Jagtap, S., and Nair, S.K. (2014) “Structure of a PL17 Family Alginate Lyase Demonstrates Functional Similarities Among Exotype Depolymerases.” J. Biol. Chem. 289, 8645-55.
    2013
  1. Lee, J., Hao, Y., Blair, P.M., Melby, J.O., Agarwal, V., Burkhart, B.J., Nair, S.K.*, and Mitchell, D.A.* (2013) “Structural and functional insight into an unexpectedly selective N-methyltransferase involved in plantazolicin biosynthesis.” Proc. Nat’l Acad. Sci. USA. 110, 12954-59. (*Corresponding author)
  1. Gonzalez-Gutierrez, G., Cuello, L.G., Nair, S.K., and Grosman, C. (2013) “Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography.” Proc. Nat’l Acad. Sci. USA. 110, 18716-21.
  1. Perry, S.L., Guha, S., Pawate, A.S., Bhaskaria, A., Agarwal, V., Nair, S.K., and Kenis, P.J. (2013) “A microfluidic approach for protein structure determination at room temperature via on-chip anomalous diffraction.” Lab Chip, 21, 3183-87.
  1. Zou, Z., Huang, B., Wu, X., Zhang, H., Qi, J., Bradner, J., Nair, S. K., and Chen, L. F. (2013) “Brd4 maintains constitutively active NF-kB in cancer cells by binding to acetylated RelA.” Oncogene, 33, 2395-404.
  1. Kelley, S. L., Lukk, T., Nair, S. K., and Tapping, R. I. (2013) “The crystal structure of human soluble CD14 reveals a bent solenoid with a hydrophobic amino-terminal pocket.” J. Immunology, 190, 1304-11.
    2012
  1. Agarwal, V., Pierce, E., McIntosh, J., Schmidt, E. W., and Nair, S. K. (2012) “Structure of cyanobactin maturation enzymes define a family of transamidating proteases.” Chem. Biol. 19, 1411-22.
  1. Agarwal, V., Lin, S., Lukk, T., Nair, S. K.* and Cronan, J. E.* (2012) “Structure of the enzyme-acyl carrier protein (ACP) substrate gatekeeper complex required for biotin synthesis.” Proc. Nat’l Acad. Sci. USA. 109, 17406-11. (*Corresponding author)
  1. Han, Y., Agarwal, V., Dodd, D., Kim, J., Bae, B., Mackie, R. I., Nair, S. K.* and Cann, I. K.* (2012) “Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus.” J. Biol. Chem. 287, 34946-60. (*Corresponding author)
  1. Li, Z., and Nair, S. K. (2012) “Quorum sensing: how bacteria can coordinate activity and synchronize their response to external signals.” Protein Sci. 21, 1403-17.
  1. Li, Z., Chen. J. H., Hao, Y., and Nair, S. K. (2012) “Structures of PelD cyclic diguanylate effector involved in pellicle formation in Pseudomonas aeruginosa PAO1.” J. Biol. Chem. 287, 30194-204.
  1. Liu, Y.L., Guerra, F., Wang, K., Wang, W., Li, J., Huang, C., Zhu, W., Houlihan, K., Li, Z., Zhang, Y., Nair, S. K., and Oldfield E. (2012) “Structure, function and inhibition of the two- and three-domain 4Fe-4S IspG proteins.” Proc. Nat’l Acad. Sci. USA. 109, 8558-63.
  1. Zou, Y., Zhang, H., Brunzelle, J., Johannes, T., Woodyer, R., Hung, J.E., Nair, N., van der Donk, W.A., Zhao, H., and Nair, S.K. (2012) “Crystal Structures of Phosphite Dehydrogenase Provide Insights into Nicotinamide Cofactor Regeneration.” Biochemistry, 51, 4263-70.
  1. Gonzalez-Gutierrez, G., Lukk, T., Agarwal, V., Papke, D., Nair, S.K., and Grosman, C. (2012) “Mutations that stabilize the open state of the Erwinia chrisanthemi ligand-gated ion channel fail to change the conformation of the pore domain in crystals.” Proc. Nat’l Acad. Sci. USA. 109, 6331-36.
  1. Garg, N., Tang, W., Goto, Y. Nair, S.K., and van der Donk, W.A. (2012) “Lantibiotics from Geobacillus thermodenitrificans.” Proc. Nat’l Acad. Sci. USA. 109, 6631-36.
  1. Lukk, T., et. al. (2012) “Homology Models Guide Discovery of Diverse Enzyme Specificities among Dipeptide Epimerases in the Enolase Superfamily.” Proc. Nat’l Acad. Sci. USA. 109, 4122-27.
  1. Agarwal, V., Tikhonov, A., Metlitskaya, A., Severinov, K., and Nair, S. K. (2012) “Structure and Function of a Serine Carboxypeptidase Adapted for Degradation of the Protein Synthesis Antibiotic Microcin C7.” Proc. Nat’l Acad. Sci. USA. 109, 4425-30.

2005 – 2011

Before 2005