Publications

Refereed Journal Publications

126. Islam MA, Tchigvintsev A, Yim V, Savchenko A, Yakunin AF, Mahadevan R, Edwards EA. Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi. Microb Biotechnol. 9:47-60, 2016.

125. Popovic A, Tchigvintsev A, Tran H, Chernikova TN, Golyshina OV, Yakimov MM, Golyshin PN, Yakunin AF. Metagenomics as a Tool for Enzyme Discovery: Hydrolytic Enzymes from Marine-Related Metagenomes. Adv Exp Med Biol. 883:1-20, 2015.

124. Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 13:722-36, 2015.

123. Placido A, Hai T, Ferrer M, Chernikova TN, Distaso M, Armstrong D, Yakunin AF, Toshchakov SV, Yakimov MM, Kublanov IV, Golyshina OV, Pesole G, Ceci LR, Golyshin PN. Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase. Appl Microbiol Biotechnol. 99:10031-46, 2015.

122. Kuznetsova E, Nocek B, Brown G, Makarova KS, Flick R, Wolf YI, Khusnutdinova A, Evdokimova E, Jin K, Tan K, Hanson AD, Hasnain G, Zallot R, de Crécy-Lagard V, Babu M, Savchenko A, Joachimiak A, Edwards AM, Koonin EV, Yakunin AF. Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS. J Biol Chem. 290:18678-98, 2015.

121. Semenova E, Kuznedelov K, Datsenko KA, Boudry PM, Savitskaya EE, Medvedeva S, Beloglazova N, Logacheva M, Yakunin AF, Severinov K. The Cas6e ribonuclease is not required for interference and adaptation by the E. coli type I-E CRISPR-Cas
system. Nucleic Acids Res. 43:6049-61, 2015.

120. Beloglazova N, Lemak S, Flick R, Yakunin AF. Analysis of nuclease activity of Cas1 proteins against complex DNA substrates. Methods Mol Biol. 1311:251-64, 2015.

119. Halavaty AS, Rich RL, Chen C, Joo JC, Minasov G, Dubrovska I, Winsor JR, Myszka DG, Duban M, Shuvalova L, Yakunin AF, Anderson WF. Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus. Acta Crystallogr D Biol Crystallogr. 71:1159-75, 2015.

118. Alcaide M, Tchigvintsev A, Martínez-Martínez M, Popovic A, Reva ON, Lafraya Á, Bargiela R, Nechitaylo TY, Matesanz R, Cambon-Bonavita MA, Jebbar M, Yakimov MM, Savchenko A, Golyshina OV, Yakunin AF, Golyshin PN, Ferrer M; MAMBA Consortium. Identification and haracterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata by using functional metagenomics. Appl Environ Microbiol. 81:2125-36, 2015.

117. Beloglazova N, Kuznedelov K, Flick R, Datsenko KA, Brown G, Popovic A, Lemak S, Semenova E, Severinov K, Yakunin AF.CRISPR RNA binding and DNA target recognition by purified Cascade complexes from Escherichia coli. Nucleic Acids Res. 43:530-43, 2015.

116. Alcaide M, Stogios PJ, Lafraya Á, Tchigvintsev A, Flick R, Bargiela R,
Chernikova TN, Reva ON, Hai T, Leggewie CC, Katzke N, La Cono V, Matesanz R, Jebbar M, Jaeger KE, Yakimov MM, Yakunin AF, Golyshin PN, Golyshina OV, Savchenko A, Ferrer M; MAMBA Consortium. Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats. Environ Microbiol. 17:332-45, 2015.

115. Tchigvintsev A, Tran H, Popovic A, Kovacic F, Brown G, Flick R, Hajighasemi M, Egorova O, Somody JC, Tchigvintsev D, Khusnutdinova A, Chernikova TN,
Golyshina OV, Yakimov MM, Savchenko A, Golyshin PN, Jaeger KE, Yakunin AF. The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes. Appl Microbiol Biotechnol. 99:2165-78, 2015.

114. Lemak S, Nocek B, Beloglazova N, Skarina T, Flick R, Brown G, Joachimiak A, Savchenko A, Yakunin AF. The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity. . Nucleic Acids Res. 42:11144-55, 2014.

113. Chen C, Joo JC, Brown G, Stolnikova E, Halavaty AS, Savchenko A, Anderson WF, Yakunin AF. Structure-based mutational studies of substrate inhibition of betaine aldehyde dehydrogenase BetB from Staphylococcus aureus. Appl Environ Microbiol. 80:3992-4002, 2014.

112. Lemak, S., Beloglazova, N., Nocek, B., Skarina, T., Flick, R., Brown, G., Popovic, A., Joachimiak, A., Savchenko, A., and Yakunin, A.F. Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S]-cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus. J. Am. Chem. Soc. 135:17476-87, 2013.

111. Tchigvintsev, A., Tchigvintsev, D., Flick, R., Popovic, A., Dong, A., Xu, X., Brown, G., Lu, W., Wu, H., Cui, H., Dombrowski, L., Joo, J.C., Beloglazova, N., Min, J., Savchenko, A., Caudy, A.A., Rabinowitz, J.D., Murzin, A.G., and Yakunin, A.F. Biochemical and structural studies of conserved Maf proteins revealed a novel family of nucleotide pyrophosphatases with a preference for modified nucleotides. Chem. Biol. 20:1386-98, 2013.

110. Anton, B.P., Chang, Y.-C., Brown, P., Choi, H.-P., Faller, L.L., Guleria, J., Hu, Z., Klitgord, N., Levy-Moonshine, A., Maksad, A., Mazumdar, V., McGettrick, M., Osmani, L., Pokrzywa, R., Rachlin, J., Swaminathan, R., Allen., B., Housman, G., Monahan, C., Rochussen, K., Tao, K., Bhagwat, A.S., Brenner, S.E., Columbus, L., de Crecy-Lagard, V., Ferguson, D., Fomenkov, A., Gadda, G., Morgan, R.D., Osterman, A.L., Rodionov, D.A., Rodionova, I.A., Rudd, K.E., Soll, D., Spain, J., Xu, S., Bateman, A., Blumenthal, R.M., Bollinger, J.M., Chang, W.-S., Ferrer, M., Friedberg, I., Galperin, M.Y., Gobeill, J., Haft, D., Hunt, J., Karp, P., Klimke, W., Krebs, C., Macelis, D., Madupu, R., Martin, M.J., Miller, J.H., O’Donovan, C., Palsson, B., Ruch, P., Setterdahl, A., Suttom, G., Tate, J., Yakunin, A., Tchigvintsev, D., Plata, G., Hu, J., Greiner, R., Horn, D., Sjolander, K., Salzberg, S.L., Vitkup, D., Letovsky, S., Segre, D., DeLisi, C., Roberts, R.J., Steffen, M., and Kasif, S. The COMBREX project: design, methodology, and initial results. PLoS Biol. 11: e1001638, 2013.

109. Kube, M., Chernikova, T.N., Al-Ramahi, Y., Beloqui, A., Lopez-Cortez, N., Guazzaroni, M.-E., Heipieper, H.J., Klages, S., Kotsyurbenko, O.R., Langer, I., Nechitaylo, T.Y., Lunsdorf, H., Fernandez, M., Juarez, S., Ciordia, S., Singer, A., Kagan, O., Egorova, O., Petit, P.A., Stogios, P., Kim, Y., Tchigvintsev, A., Flick, R., Denaro, R., Genovese, M., Albar, J.P., Reva, O.N., Martinez-Gomariz, M., Tran, H., Ferrer, M., Savchenko, A., Yakunin, A.F., Yakimov, M.M., Golyshina, O.V., Reinhardt, R., and Golyshin, P.N. Functional genome analysis of Oleispira antarctica RB-8, a key oil-degrading bacterium in cold and deep marine environments. Nature Communications. 4: article # 2156, 2013.

108. Sherif, M., Waung, D., Korbeci, B., Mavisakalyan, V., Flick, R., Brown, G., Abou-Zaid, M., Yakunin, A.F., and Master, E.R. Biochemical studies of the multicopper oxidase (SLAC) from Streptomyces coelicolor using bioactive phytochemicals and site-directed mutagenesis. Microbial Biotechnol. 6: 588-597, 2013.

107. Xu, Y.-F., Letisse, F., Absalan, F., Lu, W., Kuznetsova, E., Brown, G., Caudy, A.A., Yakunin, A.F., Broach, J.R., and Rabinowitz, J.D. Nucleotide degradation and ribose salvage in yeast. Molecular Systems Biology 9: article # 655, 2013.

106. Martinez-Martinez, M., Alcaide, M., Tchigvintsev, A., Reva, O., Polaina, J., Bargiela, R., Guazzaroni, M.E., Chicote, A., Canet, A., Valero, F., Eguizabal, E.R., Guerrero, M.D., Yakunin, A.F., and Ferrer, M. Biochemical diversity of carboxyl esterases and lipases from Lake Arreo – a metagenomic approach. Appl. Environ. Microbiol. 79: 3553-3562, 2013.

105.  Beloglazova N., Flick R., Tchigvintsev A., Brown G., Popovic A., Nocek B., and Yakunin, A.F. Nuclease Activity of the Human SAMHD1 Protein Implicated in the Aicardi-Goutieres Syndrome and HIV-1 Restriction. J. Biol. Chem. 288: 8101-8110, 2013.

104.  Zheng H., Beliavsky A., Tchigvintsev A., Brunzelle J.S., Brown G., Flick R., Evdokimova E., Wawrzak Z., Mahadevan R., Anderson W.F., Savchenko A., and Yakunin, A.F. Structure and activity of the NAD(P)+-dependent succinate semialdehyde dehydrogenase YneI from Salmonella typhimurium. Proteins 81: 1031-1041, 2013.

103.  Lemak S., Tchigvintsev A., Petit P., Flick R., Singer A.U., Brown G., Evdokimova E., Egorova O., Gonzalez C.F., Chernikova T.N., Yakimov M.M., Kube M., Reinhardt R., Golyshin P.N., Savchenko A., and Yakunin, A.F. Structure and activity of the cold-active and anion-activated carboxyl esterase OLEI01171 from the oil-degrading marine bacterium Oleispira antarctica. Biochem. J. 445: 193-203, 2012.

102.  Goacher R.E., Edwards E.A., Yakunin, A.F., Mims C.A., and Master E.R. Structure and activity of the cold-active and anion-activated carboxyl esterase OLEI01171 from the oil-degrading marine bacterium Oleispira antarctica. Anal. Chem. 84: 4443-4451, 2012.

101.  Gonzalez CF, Tchigvintsev A, Brown G, Flick R, Evdokimova E, Xu X, Osipiuk J, Cuff ME, Lynch S, Joachimiak A, Savchenko A, and Yakunin, A.F. Structure and activity of the Pseudomonas aeruginosa hotdog-fold thioesterases PA5202 and PA2801. Biochem. J. 444: 445-455, 2012.

100.  Tchigvintsev, A., Singer, A., Brown, G., Flick, R., Evdokimova, E., Tan, K., Gonzalez, C.F., Savchenko, A., and Yakunin, A.F. Biochemical and structural studies of the uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed a NAD⁺-dependent L-serine dehydrogenase. J. Biol. Chem. 287: 1874-1883, 2012.

99. Beloglazova, N., Petit, P., Flick, R., Brown, G., Savchenko, A., and Yakunin, A.F. Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J. 30: 4616-4627, 2011.

98. Lai, K.-K., Stogios, P.J., Vu, C., Xu, X., Cui, H., Molloy, S., Savchenko, A., Yakunin, A.F., and Gonzalez, C. An inserted α/β subdomain shapes the catalytic pocket of Lactobacillus johnsonii cinnamoyl esterase. PLoS One6: e23269, 2011.

97. Clasquin, M.F., Melamud, E., Singer, A., Gooding, J.R., Xu, X., Aiping, D., Cui, H., Campagna, S.R., Savchenko, A., Yakunin, A.F., Rabinowitz, J.D., and Caudy, A.A. Riboneogenesis in yeast. Cell 145: 969-980, 2011.

96. Rangarajan, E.S., Ruane, K.M., Proteau, A., Schrag, J.D., Valladares, R., Gonzalez, C.F., Gilbert, M., Yakunin, A.F., and Cygler, M. Structural and enzymatic characterization of NanS (YjhS), a 9-O-Acetyl N-acetylneuraminic acid esterase from Escherichia coli O157:H7. Protein Sci. 20: 1208-1219, 2011.

95. Tchigvintsev, A., Singer, A.U., Flick, R., Petit, P., Brown, G., Evdokimova, E., Savchenko, A., and Yakunin, A.F. Structure and activity of the Saccharomyces cerevisiae deoxyuridine triphosphate pyrophosphatase DUT1, an essential housekeeping enzyme. Biochem. J. 437: 243-253, 2011.

94. Chan, P.W.Y., Yakunin, A.F., Edwards, E.A., and Pai, E.F. Mapping the reaction coordinates of enzymatic defluorination. J. Am. Chem. Soc. 133: 7461-7468, 2011.

93. Makarova, K.S., Haft, D.H., Barrangou, R., Brouns, S., Charpentier, E., Horvath, P., Moineau, S., Mojica, F.J., Yakunin, A.F., van der Oost, J., and Koonin, E.V. Evolution and classification of the CRISPR/Cas systems.Nature Rev. Microbiol. 9: 467-477, 2011.

92. 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, E.V., Savchenko, A., Emili, A., Greenblatt, J., Edwards, A.M., and Yakunin, A.F. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair, Mol. Microbiol. 79: 484-502, 2011.

91. Syed, M.A., Koyanagi, S., Sharma, E., Jobin, M.C., Yakunin, A.F., and Levesque, C.M. The chromosomally-encoded mazEFSmu locus of Streptococcus mutans encodes a functional type II toxin-antitoxin addiction system, J. Bacteriol. 193: 1122-1130, 2011.

90. Tchigvintsev, A., Xu, X., Singer, A., Chang, C., Brown, G., Proudfoot, M., Cui, H., Flick, R., Anderson, W.F., Galperin, M.Y., Joachimiak, A., Savchenko, A., and Yakunin, A.F. Structural insight into the mechanism of cyclic di-GMP hydrolysis by EAL domain phosphodiesterases, J. Mol. Biol. 402: 524-538, 2010.

89. Cyr, T.D., She, Y.-M., Xu, X., Yakunin, A.F., Dhe-Paganon, S., Standing, K., Donald, L.J., Lee, D.C.-E., and Jia, Z. Mass spectrometry following mild enzymatic digestion reveals phosphorylation of recombinant proteins inEscherichia coli through mechanisms involving direct nucleotide binding, J. Proteome Res. 9: 3311-3318, 2010.

88. Wang, L., Mavisakalyan, V., Tillier, E.R.M., Clark, G.W., Savchenko, A., Yakunin, A.F., and Master, E. Mining bacterial genomes for novel arylesterases, Microbial Biotechnol. 3: 677-690, 2010.

87. Kuznetsova, E., Xu, L., Singer, A., Brown, G,m Dong, A., Flick, R., Cui, H., Cuff, M., Joachimiak, A., Savchenko, A., and Yakunin, A.F. Structure and activity of the metal-independent fructose 1,6-bisphosphatase YK23 fromSaccharomyces cerevisiae, J. Biol. Chem. 285: 21049-21059, 2010.

86. Chan, W.Y., Wong, M., Guthrie, J., Savchenko, A.V., Yakunin, A.F., Pai, E.F., and Edwards, E.A. Sequence- and activity-based screening of microbial genomes for novel dehalogenases, Microbial Biotechnology 3: 107-120, 2010.

85. Currie, M.A., Merino, F., Skarina, T., Wong, A.H., Singer, A., Brown, G., Savchenko, A., Caniuguir, A., Guixe, V., Yakunin, A.F., and Jia, Z. ADP-dependent 6-phosphofructokinase from Pyrococcus horikoshii OT3: structure determination and biochemical characterization of PH1645, J. Biol. Chem. 284: 22664-22671, 2009.

84. Podzelinska, K., He, S.M., Wathier, M., Yakunin, A., Proudfoot, M., Hove-Jensen, B., Zechel, D.L., and Jia, Z. Structure of PhnP: a phosphodiesterase of the carbon-phosphorous lyase pathway for phosphonate degradation, J. Biol. Chem.  284: 17216-17226, 2009.

83. Zaheer, R., Morton, R., Proudfoot, M., Yakunin, A., and Finan, T.M.   Genetic and biochemical properties of an alkaline phosphatase PhoX family protein found in many bacteria, Environ. Microbiol.  11: 1572-1587, 2009.

82. Brown, G., Singer, A., Lunin, V.V., Proudfoot, M., Skarina, T., Flick, R., Kochinyan, S., Sanishvili, R., Joachimiak, A., Edwards, A.M., Savchenko, A., and Yakunin, A.F.   Structural and biochemical characterization of the type II fructose 1,6-bisphosphatase GlpX from Escherichia coli, J. Biol. Chem. 284: 3784-3792, 2009.

81. Nocek, B., Kochinyan, S., Proudfoot, M., Brown, G., Evdokimova, E., Osipiuk, J., Edwards, A.M., Savchenko, A., Joachimiak, A., and Yakunin, A.F.   Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria, Proc. Natl. Acad. Sci. USA 105: 17730-17735, 2008.

80. Vorobiev, S.M., Su, M., Seetharaman, J., Huang, Y.J., Chen, C.X., Cunningham, K., Maglaqui, M., Owens, L., Proudfoot, M., Yakunin, A., Xiao, R., Acton, T.B., Montelione, G.T., and Tong, L.   Crystal structure of human retinoblastoma binding protein 9 (RBBP9), Proteins 74: 526-529, 2008.

79. Beloglazova, N., Brown, G., Zimmerman, M., Proudfoot, M., Makarova, K.S., Kudritska, M., Kochinyan, S., Wand, S., Chruszcz, M., Minor, W., Koonin, E.V., Edwards, A.M., Savchenko, A., and Yakunin, A.F. A novel family of sequence-specific endoribonucleases associated with the Clustered Regularly Interspaced Short Palindromic Repeats, J. Biol. Chem. 283: 20361-20371, 2008.

78. Proudfoot, M., Kuznetsova, E., Sanders, S.A., Gonzalez, C.F., Brown, G., Edwards, A.M., Arrowsmith, C.H., and Yakunin, A.F. High throughput screening of purified proteins for enzymatic activity, Methods Mol. Biol. 426: 331-341, 2008.

77. Brown, G., Singer, A., Proudfoot, M., Skarina, T., Kim, Y., Chang, C., Dementieva, I., Kuznetsova, E., Gonzalez, C., Joachimiak, A., Savchenko, A., and Yakunin, A. Functional and structural characterization of four glutaminases from Escherichia coli and Bacillus subtilis, Biochemistry 47: 5724-5735, 2008.

76. Buchko, G., Litvinova, O., Robinson, H., Yakunin, A.F., and Kennedy, M. Functional and structural characterization of DR0079 from Deinococcus radiodurans, a novel Nudix hydrolase specific for cytosine (deoxy)ribonucleoside 5`-di- and triphosphates, Biochemistry 47: 6571-6582, 2008.

75. Aceti, D., Bitto, E., Yakunin, A.F., Proudfoot, M., Bingman, C.A., Smith, D.W., Frederick, R.O., Sreenath, H.K., Vojtik, F.C., Wrobel, R.L., Fox, B.G., Markley, J.L., and Phillips, G.N.Jr. Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000, Proteins 73: 241-253, 2008.

74. Zimmerman, M., Proudfoot, M., Yakunin, A.F., and Minor, W. Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5`-deoxyribonucleotidase YfbR fromEscherichia coli, J. Mol. Biol. 378: 215-226, 2008.

73. Proudfoot, M., Sanders, S., Singer, A., Zhang, R., Brown, G., Binkowski, A., Xu, L., Lukin, J.A., Murzin, A.G., Joachimiak, A., Arrowsmith, C.H., Edwards, A.M., Savchenko, A.V., and Yakunin, A.F. Biochemical and structural characterization of a novel family of cystathionine b-synthase domain proteins fused to a Zn ribbon-like domain, J. Mol. Biol. 375: 301-315, 2008.

72. Shin, D.H., Proudfoot, M., Lim, H.J., Choi, I.K., Yokota, H., Yakunin, A.F., Kim, R., and Kim, S.-H. Structural and enzymatic characterization of DR1281: a calcineurin-like phosphoesterase from Deinococcus radiodurans,Proteins 70: 1000-1009, 2008.

71. Dong, A., Xu, X., Edwards, A.M. : Midwest Center for Structural Genomics, Chang, C., Chruszcz, M., Cuff, M., Cymborowski, M., Leo, R.D., Egorova, O., Evdokimova, E., Filippova, E., Gu, 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.: Structural Genomics Consortium, Akutsu, M., Arrowsmith, C., Avvakumov, G.V., Bochkarev, A., Dahlgren, L.G., Dhe-Paganon, S., Dimov, S., Dombrovski, L., Finerty, P. Jr., Flodin, S., Flores, A., Graslund, S., Hammerstrom, M., Herman, M.D., Hong, B.S., Hui, R., Johansson, I., Liu, Y., Nilsson, M., Nedyalkova, L., Nordlund, P., Nyman, T., Min, J., Ouyang, H., Park, H.W., Qi, C., Rabeh, W., Shen, L., Shen, Y., Sukumard, D., Tempel, W., Tong, Y., Tresagues, L., Vedadi, M., Walker, J.R., Weigelt, J., Welin, J., Wu, H., Xiao, T., Zheng, H., and Zhu, H. In situ proteolysis for protein crystallization and structure determination, Nat. Methods 4: 1019-1021, 2007.

70. Savchenko, A., Proudfoot, M., Skarina, T., Singer, A., Litvinova, O., Sanishvili, R., Brown, G., Chirgadze, N., and Yakunin, A.F. Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli, J. Mol. Biol. 374: 1091-1103, 2007.

69. Kolker, E., Hogan, J.M., Higdon, R., Kolker, N., Landorf, E., Yakunin, A.F., Collart, F.R., and van Belle, G. Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression,Proteomics 7 : 3693-3698, 2007.

68. Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., Savchenko, A., Edwards, A., White, R.H., Yakunin, A.F., and Joachimiak, A. Structural and functional studies of the Archaeoglobus fulgidusF₄₂₀:-γ-glutamyl ligase reveal a new family of the non-ribosomal peptide synthases, J. Mol. Biol.  372 : 456-469, 2007.

67. Miller, D.J., Shuvalova, L., Evdokimova, E., Savchenko, A., Yakunin, A.F., and Anderson, W.F. Structural and biochemical characterization of a novel Mn²⁺-dependent phopshodiesterase encoded by the yfcE gene, Protein Sci.16 : 1338-1348, 2007.

66. Kuznetsova, E., Proudfoot, M., Gonzalez, C.F., Brown, G., Omelchenko, M.V., Borozan, I., Carmel, L., Wolf, Y., Mori, H., Savchenko, A.V., Arrowsmith, C.H., Koonin, E.V., Edwards, A.M., and Yakunin, A.F. Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family, J. Biol. Chem. 281: 36149-36161, 2006.

65. Gonzalez, C.F., Proudfoot, M., Brown, G., Korniyenko, Y., Mori, H., Savchenko, A.V., and Yakunin, A.F.   Molecular basis of formaldehyde detoxification: characterization of two S-formylglutathione hydrolases fromEscherichia coli, J. Biol. Chem. 281: 14514-14522, 2006.

64. Xu, Q.S., Jancarik, J., Lou, Y., Kuznetsova, K., Yakunin, A.F., Yokota, H., Adams, P., Kim, R., and Kim, S.-H. Crystal structures of a phosphotransacetylase from Bacillus subtilis and its complex with acetyl phosphate, J. Struct. Funct. Genomics 6: 269-279, 2005.

63. Kuznetsova, E., Proudfoot, M., Sanders, S., Reinking, J., Savchenko, A., Arrowsmith, C.H., Edwards, A.M., and Yakunin, A.F. Enzyme genomics: application of general enzymatic screens to discover new enzymes, FEMS Microbiol. Reviews 29: 263-279, 2005.

62. Chen, S., Yakunin, A.F., Proudfoot, M., Kim, R., and Kim, S.H. Structural and functional characterization of a 5,10-methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae, Proteins 61: 433-443, 2005.

61. Proudfoot, M., Kuznetsova, E., Brown, G., Rao, N.N., Kitagawa, M., Mori, H., Savchenko, A., and Yakunin, A.F. General enzymatic screens identify three new nucleotidases in E. coli : biochemical characterization of SurE, YfbR, and YjjG, J. Biol. Chem. 279: 54687-54694, 2004.

60. Yakunin, A.F., Proudfoot, M., Kuznetsova, E., Savchenko, A., Brown, G., Arrowsmith, C.H., and Edwards, A.M.   The HD domain of the Escherichia coli tRNA nucleotidyltransferase has 2`,3`-cyclic phosphodiesterase, 2`-nucleotidase, and phosphatase activities, J. Biol. Chem. 279: 36819-36827, 2004.

59. Chen, S., Yakunin, A.F., Kuznetsova, E., Busso, D., Pufan, R., Proudfoot, M., Kim, R., and Kim, S.-H. Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii, J. Biol. Chem.279: 31854-31862, 2004.

58. Yakunin, A.F., Yee, A.A., Savchenko, A., Edwards, A.M., and Arrowsmith, C.H. Structural   proteomics: a tool for genome annotation, Curr. Opin. Chem. Biol. 8: 42-48, 2004.

57. Saridakis, V., Yakunin, A., Xu, X., Anandakumar, P., Pennycooke, M., Gu, J., Cheung, F., Lew, J.M., Sanishvili, R., Joachimiak, A., Arrowsmith, C.H., Christendat, D., and Edwards, A.M.   The structural basis for methylmalonic aciduria: the crystal structure of archaeal ATP:cobalamin adenosyltransferase, J. Biol. Chem. 279: 23646-23653, 2004.

56. Xia, L., Yakunin, A.F., and McKay, R.M.L.   Fe-responsive accumulation of redox proteins ferredoxin and flavodoxin in a marine cryptomonad, Eur. J. Phycol. 39: 73-82, 2004.

55. Kim, Y., Yakunin, A.F.,  Kuznetsova, E., Xu, X., Pennycooke, M., Gu, J., Cheung, F., Proudfoot, M., Arrowsmith, C.H., Joachimiak, A., Edwards, and A., Christendat, D.   Structure and function based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum, J. Biol. Chem. 279: 517-526, 2004.

54. Sanishvili, R.^*, Yakunin, A.F.^*(equal contribution), Laskowski, R., Skarina, T., Evdokimova, E., Doherty-Kirby, A., Lajoie, G.A., Thornton, J.M., Arrowsmith, C.H., Savchenko, A., Joachimiak, A., and Edwards, A.M. Integrating structure, bioinformatics and enzymology to discover function: BioH, a new carboxylesterase from E. coli, J. Biol. Chem. 278: 26039-26045, 2003.

53. Drepper, T.,  Gross, S., Yakunin, A.F., Hallenbeck, P.C., Masepohl, B., and Klipp, W. Role of GlnB and GlnK in ammonium control of both nitrogenase systems in the phototrophic bacterium Rhodobacter capsulatus,Microbiology 149: 2203-2212, 2003.

52. Yang, Z., Savchenko, A., Yakunin, A.F., Zhang, R., Edwards, A., Arrowsmith C., and Tong, L.   Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643, J. Biol. Chem. 278: 8804-8808, 2003.

51. Yakunin, A.F., and Hallenbeck, P.C. AmtB is necessary for NH₄⁺-induced nitrogenase switch-off and ADP-ribosylation in Rhodobacter capsulatus, J. Bacteriol. 184: 4081-4088, 2002.

50. Yakunin, A.F., Fedorov, A.S., Laurinavichene, T.V., Glaser, V.M., Egorov, N.S., Tsygankov, A.A., Zinchenko, V.V., and Hallenbeck, P.C. Regulation of nitrogenase in the photosynthetic bacterium Rhodobacter sphaeroidescontaining   draTG and nifHDK genes from Rhodobacter capsulatus, Can. J. Microbiol. 47: 206-212, 2001.

49. Yakunin, A.F., and Hallenbeck, P.C.  Regulation of nitrogenase activity in Rhodobacter capsulatus under dark microoxic conditions , Arch. Microbiol.  173: 366-372, 2000.

48. McKay, R.M.L., La Roche, J., Yakunin, A.F., Durnford, D.G., and Geider, R.J. Accumulation of ferredoxin and flavodoxin in a marine diatom in response to Fe, J. Phycol. 35: 510-519, 1999.

47. Yakunin, A.F., T.V. Laurinavichene, A.A. Tsygankov, and P.C. Hallenbeck. The presence of  ADP-ribosylated Fe-protein of nitrogenase is correlated with cellular nitrogen status, J. Bacteriol.  181: 1994-2000, 1999.

46. Yakunin, A.F., and Hallenbeck, P.C. Short-term nitrogenase regulation in Rhodobacter capsulatus: multiple in vivo nitrogenase responses to NH₄⁺ addition, J. Bacteriol., 180: 6392-6395, 1998.

45. Yakunin, A.F., and Hallenbeck, P.C. Purification and properties of a pyruvate oxidoreductase from the photosynthetic bacterium Rhodobacter capsulatus, Biochim. Biophys. Acta 1409: 39-49, 1998.

44. Yakunin, A.F., and Hallenbeck, P.C. A luminol/iodophenol chemiluminescent detection system for Western immunoblots, Anal. Biochem. 258: 146-149, 1998.

43. Yakunin, A.F., and Hallenbeck, P.C.  Regulation of the synthesis of pyruvate carboxylase in the photosynthetic bacterium Rhodobacter capsulatus, J. Bacteriol. 179: 1460‑1468, 1997.

42. Gennaro, G., Hübner, P., Sandmeier, U., Yakunin, A.F., and Hallenbeck, P.C. Cloning, characterization and regulation of nifF from Rhodobacter capsulatus, J. Bacteriol. 178: 3949-3952, 1996.

41. Yakunin, A.F., Troshina, O.Y., and Gogotov, I.N.  Relationship between nitrogenase                    synthesis and C/N ratio in nitrogen-fixing cyanobacterium Anabaena variabilis, Microbiology     (Moscow) 64: 10-12, 1995.

40. Yakunin, A.F., Gennaro, G., and Hallenbeck, P.C. Purification and properties of a nif specific flavodoxin from the photosynthetic bacterium, Rhodobacter capsulatus, J. Bacteriol. 175: 6775-6780, 1993.

39. Tamagnini, P., Yakunin, A.F., Gogotov, I.N., and Lindblad, P. Plant-type and bacterial-type ferredoxins in a nitrogen-fixing cyanobacterium: Nostoc sp. strain PCC 73102, FEMS Microbiol. Lett. 107: 37-42, 1993.

38. Yakunin, A.F., Troshina, O.Y., and Gogotov, I.N.  Properties and regulation of synthesis of flavodoxin from nitrogen-fixing cyanobacterium Anabaena sphaerica,  Microbiology (Moscow) 62: 83-89, 1993.

37. Yakunin, A.F., and Gogotov, I.N.  Natural electron donors for nitrogenase in cyanobacterium Anabaena variabilis,  Microbiology (Moscow) 62: 76-82, 1993.

36. Yakunin, A.F., Hallenbeck, P.C., Troshina, O.Y., and Gogotov, I,N. Purification and properties of a flavodoxin from the heterocystous cyanobacterium, Anabaena sphaerica,  Biochim. Biophys. Acta 1164: 305-310, 1993.

35. Yakunin, A.F., Hallenbeck, P.C., Troshina, O.Y., and Gogotov, I.N. Purification and properties of a bacterial-type ferredoxin from the nitrogen-fixing cyanobacterium Anabaena variabilis ATCC 29413,  Biochim. Biophys. Acta1163: 124-130, 1993.

34. Troshina, O.Yu., Yakunin, A.F., and Gogotov, I.N. Growth and the activity of the enzymes of nitrogen metabolism in free-living cultures of Anabaena azollae and its mutants resistant to ethylene diamine,  Microbiology (Moscow) 61: 1004-1010, 1992.

33. Laurinavichene, T.V., Yakunin, A.F., and Gogotov, I.N. Nitrogenase activity and growth of nitrogen-fixing symbiotic association Azolla caroliniana under the deficiency of some elements, Microbiology (Moscow) 61: 858-864, 1992.

32. Yakunin, A.F., Troshina, O.Y., Jha, M., and Gogotov, I.N. Effect of ammonium on nitrogenase activity in the heterocystous cyanobacterium Anabaena variabilis,  Microbiology (Moscow) 61: 256-260, 1992.

31. Yakunin, A.F., Chan, V.N., and Gogotov, I.N.  Synthesis of two ferredoxins and nitrogenase by the heterocystic cyanobacterium Anabaena sphaerica,  Microbiology (Moscow) 60: 622-627, 1991.

30. Yakunin, A.F., Laurinavichene, T.V., Chan, K., and Gogotov, I.N. Nitrate reductases from Rhodobacter capsulatus B10 and Anabaena variabilis,  Microbiology (Moscow) 60: 423-430, 1991.

29. Yakunin, A.F., Chan, V.N., and Gogotov, I.N.  Dependence of growth and synthesis of different nitrogenases in Anabaena variabilis on the presence of molybdenum, vanadium and tungsten in the medium, Microbiology(Moscow) 60: 71-76, 1991.

28. Yakunin, A.F., Chan, K., and Gogotov, I.N.  Effect of molybdenum on the growth, nitrogenase and nitrate reductase activities of the heterocystic cyanobacterium Anabaena sphaerica,  Microbiology (Moscow) 59: 956-961, 1990.

27. Yakunin, A.F., Jha, M., and Gogotov, I.N. Effect of ammonium on the nitrogenase activity of heterocystic cyanobacterium Anabaena variabilis,  Proc. USSR Acad. Sci. 315: 748-750, 1990.

26. Chan, V.N., Nguen, S.T., Yakunin, A.F., and Gogotov, I.N. Effect of cyanobacterium Aphanothece pallida on soil fertility and rice crop, Agrochemistry (Moscow) 8: 14-19, 1990.

25. Yakunin, A.F., Chan, K., and Gogotov, I.N. The growth, nitrogenase and nitrate reductase activities of Anabaena sphaerica at a deficiency of certain ions in the medium,  Microbiology (Moscow) 59: 771-775, 1990.

24. Chan, V.N., Yakunin, A.F., and Gogotov, I.N.  Effect of molybdenum, vanadium and tungsten on the growth and synthesis of nitrogenase in free-living Anabaena azollae,  Microbiology (Moscow) 59: 583-586, 1990.

23. Chan, V.N., Yakunin, A.F., and Gogotov, I.N. Effect of combined nitrogen on the growth and synthesis of different nitrogenases in Anabaena variabilis, Microbiology (Moscow) 59: 394-398, 1990.

22. Chan, V.N., Yakunin, A.F., and Gogotov, I.N. Effect of fructose on the growth and synthesis of nitrogenase of heterocystic cyanobacterium Anabaena sphaerica,  Microbiology (Moscow) 59: 245-248, 1990.

21. Yakunin, A.F., Chan, K., and Gogotov, I.N. Purification and properties of two ferredoxins of the nitrogen-fixing heterocystic cyanobacterium Anabaena sphaerica,  Biochemistry (Moscow) 55: 80-86, 1990.

20. Laurinavichene, T.V., Yakunin, A.F., and Gogotov, I.N. Effect of temperature and photoperiod on the growth and nitrogen fixation of Azolla,  Plant. Physiol. (Moscow) 37: 457-461, 1990.

19. Laurinavichene, T.V., Yakunin, A.F., and Gogotov, I.N. Growth and activities of nitrogenase and nitrate reductase in Azolla, containing and not containing Anabaena, Plant. Physiol. (Moscow) 36: 318-323, 1989.

18. Chan, V.N., Yakunin, A.F., and Gogotov, I.N. Capacity of the free-living cyanobacterium Anabaena azollae to synthesize the alternative nitrogenases,  Proc. USSR Acad. Sci. 309: 1480-1482, 1989.

17. Yakunin, A.F., Chan, V.N., and Gogotov, I.N. Synthesis of the alternative nitrogenases by heterocystic cyanobacterium Anabaena variabilis,  Proc. USSR Acad. Sci. 307: 1269-1271, 1989.

16. Kreslavsky, V.D., Makarov, A.D., Brandt, A.B., Kiseleva, M.I., Mukhin, E.N., Rusieva, R.K., Yakunin, A.F., and Rudenko, T.I.  Effect of red light, phytohormones, and dichlorophenylurea derivatives on ethylene evolution byChlorella, Plant Physiol. (Moscow) 35: 1162-1169, 1988.

15. Chan, K., Yakunin, A.F., and Gogotov, I.N. Influence of different forms of bound nitrogen on growth and nitrogenase activity of cyanobacteria isolated from Vietnamese rice paddy soil, Microbiology (Moscow) 57: 972-976, 1988.

14. Yakunin, A.F. and Gogotov, I.N. Formation of two forms of nitrogenase and effect of its switch-off by ammonia in purple bacteria, Microbiol. Sci. 5: 78-81, 1988.

13. Yakunin, A.F., Tsygankov, A.A., Troshina, O.Y., and Gogotov, I.N. Synthesis of two forms of nitrogenase and activity of the enzymes of assimilation of ammonium in a continuous culture of Ectothiorhodospira shaposhnikovii,Proc. USSR Acad. Sci. 300: 1009-1012, 1988.

12. Yakunin, A.F. and Gogotov, I.N. Possible functions of two ferredoxins in the metabolism of the purple non-sulphur bacterium Rhodobacter capsulatus B10, Biochemistry (Moscow) 52: l977-1982, 1987.

11. Yakunin, A.F., Tsygankov, A.A., and Gogotov, I.N.  Regulation of two nitrogenase forms in a continuous culture of Rhodobacter capsulatus, Microbiology (Moscow) 56: 916-921, 1987.

10. Yakunin, A.F., Tsygankov, A.A., Gogotov, I.N., and L’vov, N.P. The dependence of nitrogenase and nitrate reductase activities on the concentration of molybdenum in the medium and nitrate assimilation in Rhodopseudomonas capsulata cells, Microbiology (Moscow) 55: 564-569, 1986.

9. Yakunin, A.F., Tsygankov, A.A., and Gogotov, I.N.  The ratio of two forms of nitrogenase and effect of its switch-off in ammonia-limited cells of Rhodopseudomonas capsulata, Proc. USSR Acad. Sci. 281: 482-485, 1985.

8. Yakunin, A.F., Hoang, T., and Gogotov, I.N.  Purification and properties of two ferredoxins from water fern Azolla pinnata,  Biochemistry (Moscow) 50: 514-520, 1985.

7. Yakunin, A.F.  and Gogotov, I.N. The activity of two forms of nitrogenase from Rhodopseudomonas capsulata in the presence of different electron donors,  FEMS Microbiol. Lett. 23: 217-220, 1984.

6.  Yakunin, A.F. and Gogotov, I.N.  Properties and regulation of synthesis of two ferredoxins from Rhodopseudomonas capsulata, Biochim. Biophys. Acta 725: 298-308, 1983.

5. Yakunin, A.F., and Gogotov, I.N.  Properties of two ferredoxin forms from Rhodopseudomonas capsulata, Biochemistry (Moscow) 48: 811-817, 1983.

4. Tsygankov, A.A., Yakunin, A.F., and Gogotov, I.N. The effect of pO2 on the growth and hydrogenase and nitrogenase activities of Rhodopseudomonas capsulata and Azotobacter vinelandii cells, Microbiology (Moscow) 52: 543-547, 1983.

3. Tsygankov, A.A., Yakunin, A.F., and Gogotov, I.N. Hydrogenase activity of Rhodopseudomonas capsulata growing in organic media, Microbiology (Moscow) 51: 533-537, 1982.

2. Kulakova, S.M., Yakunin, A.F., and Gogotov, I.N.  Resistance of hydrogenase and nitrogenase of purple bacteria to oxygen and products of its reduction, Appl. Biochem. Microbiol. (Moscow) 18: 324-330, 1982.

1. Zajtseva, G.N., Yakunin, A.F., D.A. Maslov, D.A., Kuz’min, E.V., and Zograf, Y.N.  Polypeptide synthesis dependent on kinetoplast DNA from Crithidia oncopelti in a cell-free system of E. coli, Biochemistry (Moscow) 46: 2056-2063, 1981.