Erratum: Structural and biochemical insight into the mechanism of Rv2837c from Mycobacterium tuberculosis as a c-di-NMP phosphodiesterase (Journal of Biological Chemistry (2016) 291 (3668–3681) DOI: 10.1074/jbc.M115.699801);Structural and biochemical insight into the mechanism of Rv2837c from mycobacterium tuberculosis as a c-di-NMP phosphodiesterase

Journal of Biological Chemistry

Volumn 291, Issue 7, 2016, Pages 3668-3681

  He, Qing ^a   Wang, Feng ^a   Liu, Shiheng ^a   Zhu, Deyu ^a   Cong, Hengjiang ^a   Gao, Fei ^a   Li, Bingqing ^a   Wang, Hongwei ^a   Lin, Zong ^b   Liao, Jun ^c   Gu, Lichuan ^a  

^a SHANDONG UNIVERSITY   (China)

^b TSINGHUA UNIVERSITY   (China)

^c SHANGHAITECH UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CELL SIGNALING; CRYSTAL STRUCTURE; ESTERS;

BACTERIAL CELLS; CATALYTIC DEGRADATION; CAUSATIVE AGENTS; DINUCLEOTIDES; M. TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS; PHOSPHODIESTERASES; SIGNALING PATHWAYS;

TUBES (COMPONENTS);

CYCLIC AMP PHOSPHODIESTERASE; CYCLIC GMP PHOSPHODIESTERASE; PHOSPHODIESTERASE; PHOSPHODIESTERASE RV2837C; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; BIS(3',5')-CYCLIC DIGUANYLIC ACID; CYCLIC AMP; CYCLIC DIADENOSINE PHOSPHATE; CYCLIC GMP; DINUCLEOSIDE PHOSPHATE; EXORIBONUCLEASE; HYBRID PROTEIN; OLIGORIBONUCLEASE; PEPTIDE FRAGMENT; RECOMBINANT PROTEIN;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DOWN REGULATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME DEGRADATION; ENZYME STRUCTURE; INTRACELLULAR SIGNALING; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN HYDROLYSIS; AMINO ACID SEQUENCE; ANALOGS AND DERIVATIVES; BIOCATALYSIS; CHEMISTRY; CONSERVED SEQUENCE; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; MOLECULAR MODEL; MUTATION; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT;

3',5'-CYCLIC-AMP PHOSPHODIESTERASES; 3',5'-CYCLIC-GMP PHOSPHODIESTERASES; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BIOCATALYSIS; CATALYTIC DOMAIN; CONSERVED SEQUENCE; CYCLIC AMP; CYCLIC GMP; DINUCLEOSIDE PHOSPHATES; EXORIBONUCLEASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; MYCOBACTERIUM TUBERCULOSIS; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; RECOMBINANT FUSION PROTEINS; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

EID: 84964497482     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/JBC.A115.699801     Document Type: Erratum

References (41)

1. Zumla, A., George, A., Sharma, V., Herbert, R. H., Baroness Masham of Ilton, Oxley, A., and Oliver, M. (2015) TheWHO2014 global tuberculosis report: further to go [J]. Lancet Global Health 3, e10-e12.
2. Dey, B., Dey, R. J., Cheung, L. S., Pokkali, S., Guo, H., Lee, J. H., and Bishai, W. R. (2015) A bacterial cyclic dinucleotide activates the cytosolic surveillance pathway and mediates innate resistance to tuberculosis. Nat. Med. 21, 401-406.
3. Gomelsky, M. (2011) cAMP, c-di-GMP, c-di-AMP and now cGMP: bacteria use them all! Mol. Microbiol. 79, 562-565.
4. Kalia, D., Merey, G., Nakayama, S., Zheng, Y., Zhou, J., Luo, Y., Guo, M., Roembke, B. T., and Sintim, H. O. (2013) Nucleotide, c-di-GMP, c-di- AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis. Chem. Soc. Rev. 42, 305-341.
5. Gao, J., Tao, J., Liang, W., Zhao, M., Du, X., Cui, S., Duan, H., Kan, B., Su, X., and Jiang, Z. (2015) Identification and characterization of phosphodiesterases that specifically degrade 3- 3-cyclic GMP-AMP. Cell Res. 25, 539-550.
6. Römling, U., Gomelsky, M., and Galperin, M. Y. (2005) c-di-GMP: The dawning of a novel bacterial signalling system. Mol. Microbiol. 57, 629-639.
7. Hengge, R. (2009) Principles of c-di-GMP signalling in bacteria. Nat. Rev. Microbiol. 7, 263-273.
8. Burdette, D. L., Monroe, K. M., Sotelo-Troha, K., Iwig, J. S., Eckert, B., Hyodo, M., Hayakawa, Y., and Vance, R. E. (2011) STING is a direct innate immune sensor of cyclic di-GMP. Nature 478, 515-518.
9. Römling, U., Galperin, M. Y., and Gomelsky, M. (2013) Cyclic di-GMP: The first 25 years of a universal bacterial second messenger. Microbiol. Mol. Biol. Rev. 77, 1-52.
10. Bejerano-Sagie, M., Oppenheimer-Shaanan, Y., Berlatzky, I., Rouvinski, A., Meyerovich, M., and Ben-Yehuda, S. (2006) A checkpoint protein that scans the chromosome for damage at the start of sporulation in Bacillus subtilis. Cell 125, 679-690.
11. Zhang, L., Li, W., and He, Z.-G. (2013) DarR, a TetR-like transcriptional factor, is a cyclic di-AMP-responsive repressor in Mycobacterium smegmatis. J. Biol. Chem. 288, 3085-3096.
12. Witte, C. E., Whiteley, A. T., Burke, T. P., Sauer, J.-D., Portnoy, D. A., and Woodward, J. J. (2013) Cyclic di-AMP is critical for Listeria monocytogenes growth, cell wall homeostasis, and establishment of infection. mBio 4, e00282-00213.
13. Oppenheimer-Shaanan, Y., Wexselblatt, E., Katzhendler, J., Yavin, E., and Ben-Yehuda, S. (2011) c-di-AMP reports DNA integrity during sporulation in Bacillus subtilis. EMBO Rep. 12, 594-601.
14. Corrigan, R. M., Campeotto, I., Jeganathan, T., Roelofs, K. G., Lee, V. T., and Gründling, A. (2013) Systematic identification of conserved bacterial c-di-AMP receptor proteins. Proc. Natl. Acad. Sci. U.S.A. 110, 9084-9089.
15. Yang, J., Bai, Y., Zhang, Y., Gabrielle, V. D., Jin, L., and Bai, G. (2014) Deletion of the cyclic di-AMP phosphodiesterase gene (cnpB) in Mycobacterium tuberculosis leads to reduced virulence in a mouse model of infection. Mol. Microbiol. 93, 65-79.
16. Bai, Y., Yang, J., Eisele, L. E., Underwood, A. J., Koestler, B. J., Waters, C. M., Metzger, D. W., and Bai, G. (2013) Two DHH subfamily 1 proteins in Streptococcus pneumoniae possess cyclic di-AMP phosphodiesterase activity and affect bacterial growth and virulence. J. Bacteriol. 195, 5123-5132.
17. Manikandan, K., Sabareesh, V., Singh, N., Saigal, K., Mechold, U., and Sinha, K. M. (2014) Two-step synthesis and hydrolysis of cyclic di-AMP in Mycobacterium tuberculosis. PLoS One 9, e86096.
18. Huynh, T. N., Luo, S., Pensinger, D., Sauer, J. D., Tong, L., and Woodward, J. J. (2015) An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence. Proc. Natl. Acad. Sci. U.S.A. 112, E747-E756.
19. Rao, F., See, R. Y., Zhang, D., Toh, D. C., Ji, Q., and Liang, Z.-X. (2010) YybT is a signaling protein that contains a cyclic dinucleotide phosphodiesterase domain and aGGDEFdomain with ATPase activity. J. Biol. Chem. 285, 473-482.
20. Ye, M., Zhang, J. J., Fang, X., Lawlis, G. B., Troxell, B., Zhou, Y., Gomelsky, M., Lou, Y., and Yang, X. F. (2014) DhhP, a cyclic di-AMP phosphodiesterase of Borrelia burgdorferi, is essential for cell growth and virulence. Infect. Immun. 82, 1840-1849.
21. Postic, G., Danchin, A., and Mechold, U. (2012) Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae. RNA 18, 155-165.
22. Srivastav, R., Kumar, D., Grover, A., Singh, A., Manjasetty, B. A., Sharma, R., and Taneja, B. (2014) Unique subunit packing in mycobacterial nano- RNase leads to alternate substrate recognitions in DHH phosphodiesterases. Nucleic Acids Res. 42, 7894-7910.
23. Dey, B., and Bishai, W. R. (2014) Crosstalk between Mycobacterium tuberculosis and the host cell. Semin. Immunol. 26, 486-496.
24. Kumar, M., and Chatterji, D. (2008) Cyclic di-GMP: A second messenger required for long-term survival, but not for biofilm formation, in Mycobacterium smegmatis. Microbiology 154, 2942-2955.
25. Otwinowski, Z., and Minor, W. (1997) Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
26. Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L. W., Kapral, G. J., Grosse-Kunstleve, R. W., Mc- Coy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C., and Zwart, P. H. (2010) PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221.
27. Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A., and Wilson, K. S. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235-242.
28. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F., and Vagin, A. A. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355-367.
29. Emsley, P., Lohkamp, B., Scott, W. G., and Cowtan, K. (2010) Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501.
30. Burhenne, H., and Kaever, V. (2013) Quantification of cyclic dinucleotides by reversed-phase LC-MS/MS. Methods Mol. Biol. 1016, 27-37.
31. Zhu, D., Wang, L., Shang, G., Liu, X., Zhu, J., Lu, D., Wang, L., Kan, B., Zhang, J. R., and Xiang, Y. (2014) Structural biochemistry of a Vibrio cholerae dinucleotide cyclase reveals cyclase activity regulation by folates. Mol. Cell 55, 931-937.
32. Holm, L., and Rosenström, P. (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, W545-W549.
33. Tang, Q., Luo, Y., Zheng, C., Yin, K., Ali, M. K., Li, X., and He, J. (2015) Functional analysis of a c-di-AMP-specific phosphodiesterase MsPDE from Mycobacterium smegmatis. Int. J. Biol. Sci. 11, 813-824.
34. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., and Olson, A. J. (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput Chem. 30, 2785-2791.
35. Römling, U., and Amikam, D. (2006) Cyclic di-GMP as a second messenger. Curr. Opin Microbiol. 9, 218-228.
36. Gentner, M., Allan, M. G., Zaehringer, F., Schirmer, T., and Grzesiek, S. (2012) Oligomer formation of the bacterial second messenger c-di-GMP: Reaction rates and equilibrium constants indicate a monomeric state at physiological concentrations. J. Am. Chem. Soc. 134, 1019-1029.
37. Egli, M., Gessner, R. V., Williams, L. D., Quigley, G. J., van der Marel, G. A., van Boom, J. H., Rich, A., and Frederick, C. A. (1990) Atomic-resolution structure of the cellulose synthase regulator cyclic diguanylic acid. Proc. Natl. Acad. Sci. U.S.A. 87, 3235-3239.
38. Guan, Y., Gao, Y. G., Liaw, Y. C., Robinson, H., and Wang, A. H. (1993) Molecular structure of cyclic diguanylic acid at 1 A resolution of two crystal forms: self-association, interactions with metal ion/planar dyes and modeling studies. J. Biomol. Struct. Dyn. 11, 253-276.
39. Sultan, S. Z., Pitzer, J. E., Boquoi, T., Hobbs, G., Miller, M. R., and Motaleb, M. A. (2011) Analysis of the HD-GYP domain cyclic dimeric GMP phosphodiesterase reveals a role in motility and the enzootic life cycle of Borrelia burgdorferi. Infect. Immun. 79, 3273-3283.
40. Corrigan, R. M., Abbott, J. C., Burhenne, H., Kaever, V., and Gründling, A. (2011). c-di-AMP is a new second messenger in Staphylococcus aureus with a role in controlling cell size and envelope stress. PLoS Pathog. 7, e1002217.
41. Bharati, B. K., Sharma, I. M., Kasetty, S., Kumar, M., Mukherjee, R., and Chatterji, D. (2012) A full-length bifunctional protein involved in c-di- GMP turnover is required for long-term survival under nutrient starvation in Mycobacterium smegmatis. Microbiology 158, 1415-1427.