Structural study of MCPIP1 N-terminal conserved domain reveals a PIN-like RNase

Nucleic Acids Research

Volumn 40, Issue 14, 2012, Pages 6957-6965

  Xu, Jiwei ^a,b   Peng, Wei ^a   Sun, Yao ^a,b   Wang, Xiangxi ^a,b   Xu, Yihui ^a   Li, Xuemei ^a   Gao, Guangxia ^a   Rao, Zihe ^a  

^a INSTITUTE OF BIOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; AMINO TERMINAL TELOPEPTIDE; MONOCYTE CHEMOTACTIC PROTEIN 1; MONOCYTE CHEMOTACTIC PROTEIN 1 INDUCED PROTEIN 1; PIN LIKE RIBONUCLEASE; RIBONUCLEASE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CATALYSIS; CONTROLLED STUDY; ENZYME ACTIVITY; ESCHERICHIA COLI; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN RNA BINDING; PROTEIN STRUCTURE; RNA DEGRADATION; SITE DIRECTED MUTAGENESIS; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

3' UNTRANSLATED REGIONS; AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CATALYTIC DOMAIN; CONSERVED SEQUENCE; HUMANS; INTERLEUKIN-6; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEASES; RNA; TRANSCRIPTION FACTORS;

EID: 84864940861     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks359     Document Type: Article

References (39)

1. Janeway, C.A. Jr. and Medzhitov, R. (2002) Innate immune recognition. Annu. Rev. Immunol., 20, 197-216. (Pubitemid 34293424)
2. Liu, F. and Gu, J. (2011) Retinoic acid inducible gene-I, more than a virus sensor. Protein Cell, 2, 351-357.
3. Skalniak, L., Mizgalska, D., Zarebski, A., Wyrzykowska, P., Koj, A. and Jura, J. (2009) Regulatory feedback loop between NF-kappaB and MCP-1-induced protein 1 RNase. FEBS J., 276, 5892-5905.
4. Zhou, L., Azfer, A., Niu, J., Graham, S., Choudhury, M., Adamski, F.M., Younce, C., Binkley, P.F. and Kolattukudy, P.E. (2006) Monocyte chemoattractant protein-1 induces a novel transcription factor that causes cardiac myocyte apoptosis and ventricular dysfunction. Circ. Res., 98, 1177-1185. (Pubitemid 43948104)
5. Jura, J., Wegrzyn, P., Korostynski, M., Guzik, K., Oczko-Wojciechowska, M., Jarzab, M., Kowalska, M., Piechota, M., Przewlocki, R. and Koj, A. (2008) Identification of interleukin-1 and interleukin-6-responsive genes in human monocyte-derived macrophages using microarrays. Biochim. Biophys. Acta, 1779, 383-389. (Pubitemid 351847863)
6. Liang, J., Song, W., Tromp, G., Kolattukudy, P.E. and Fu, M. (2008) Genome-wide survey and expression profiling of CCCH-zinc finger family reveals a functional module in macrophage activation. PLoS One, 3, e2880.
7. Liang, J., Wang, J., Azfer, A., Song, W., Tromp, G., Kolattukudy, P.E. and Fu, M. (2008) A novel CCCH-zinc finger protein family regulates proinflammatory activation of macrophages. J. Biol. Chem., 283, 6337-6346.
8. Matsushita, K., Takeuchi, O., Standley, D.M., Kumagai, Y., Kawagoe, T., Miyake, T., Satoh, T., Kato, H., Tsujimura, T., Nakamura, H. et al. (2009) Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. Nature, 458, 1185-1190.
9. Mizgalska, D., Wegrzyn, P., Murzyn, K., Kasza, A., Koj, A., Jura, J. and Jarzab, B. (2009) Interleukin-1-inducible MCPIP protein has structural and functional properties of RNase and participates in degradation of IL-1beta mRNA. FEBS J., 276, 7386-7399.
10. Suzuki, H.I., Arase, M., Matsuyama, H., Choi, Y.L., Ueno, T., Mano, H., Sugimoto, K. and Miyazono, K. (2011) MCPIP1 ribonuclease antagonizes dicer and terminates microRNA biogenesis through precursor microRNA degradation. Mol. Cell, 44, 424-436.
11. Hudson, B.P., Martinez-Yamout, M.A., Dyson, H.J. and Wright, P.E. (2004) Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d. Nat. Struct. Mol. Biol., 11, 257-264. (Pubitemid 38282771)
12. Lai, W.S., Kennington, E.A. and Blackshear, P.J. (2002) Interactions of CCCH zinc finger proteins with mRNA: non-binding tristetraprolin mutants exert an inhibitory effect on degradation of AU-rich element-containing mRNAs. J. Biol. Chem., 277, 9606-9613. (Pubitemid 34953050)
13. Hake, L.E., Mendez, R. and Richter, J.D. (1998) Specificity of RNA binding by CPEB: requirement for RNA recognition motifs and a novel zinc finger. Mol. Cell. Biol., 18, 685-693. (Pubitemid 28063401)
14. Bidzhekov, K., Zernecke, A. and Weber, C. (2006) MCP-1 induces a novel transcription factor with proapoptotic activity. Circ. Res., 98, 1107-1109. (Pubitemid 43948092)
15. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326. (Pubitemid 27085611)
16. Strong, M., Sawaya, M.R., Wang, S., Phillips, M., Cascio, D. and Eisenberg, D. (2006) Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA, 103, 8060-8065. (Pubitemid 43801052)
17. Pape, T.S. and Schneider, T.R. (2004) HKL2MAP: a graphical user interface for phasing with SHELX programs. J. Appl. Crystallogr., 37, 843-844.
18. Schneider, T.R. and Sheldrick, G.M. (2002) Substructure solution with SHELXD. Acta Crystallogr. D Biol. Crystallogr., 58, 1772-1779. (Pubitemid 35169744)
19. Sheldrick, G.M. (2002) Macromolecular phasing with SHELXE. Z Kristallogr., 217, 644-650.
20. Sheldrick, G.M. (2003) SHELXC. Goettingen University.
21. McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C. and Read, R.J. (2007) Phaser crystallographic software. J. Appl. Crystallogr., 40, 658-674. (Pubitemid 47080256)
22. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr., 50, 760-763.
23. Afonine, P.V., Grosse-Kunstleve, R.W. and Adams, P.D. (2005) CCP4 Newsl., 42, http://www.ccp4.ac.uk/newsletters/newsletter42/content.html.
24. Emsley, P., Lohkamp, B., Scott, W.G. and Cowtan, K. (2010) Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr., 66, 486-501.
25. DeLano, W.L. (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA.
26. Huang, Z., Wang, X. and Gao, G. (2010) Analyses of SELEX-derived ZAP-binding RNA aptamers suggest that the binding specificity is determined by both structure and sequence of the RNA. Protein Cell, 1, 752-759.
27. Jie, L.I., Yutao, Y.A.N.G., Keqian, M.A., Zhuqing, Y.A.N., Xiaoxiao, L.I., Chunli, Z.H.A.O. and Zhiqing, X. (2011) Cloning and preliminary functional analysis of human galanin receptor 2 promoter. Acta Biophys. Sin., 27, 417-423.
28. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2. Bioinformatics, 23 2947-2948.
29. Gouet, P., Courcelle, E., Stuart, D.I. and Metoz, F. (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics, 15, 305-308. (Pubitemid 29213756)
30. Matthews, B.W. (1968) Solvent content of protein crystals. J. Mol. Biol., 33, 491-497.
31. Ceska, T.A., Sayers, J.R., Stier, G. and Suck, D. (1996) A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease. Nature, 382, 90-93. (Pubitemid 26243365)
32. Holm, L. and Rosenstrom, P. (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res., 38, W545-W549.
33. Glavan, F., Behm-Ansmant, I., Izaurralde, E. and Conti, E. (2006) Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. EMBO J., 25, 5117-5125. (Pubitemid 44658529)
34. Harding, M.M. (1999) The geometry of metal-ligand interactions relevant to proteins. Acta Crystallogr. D Biol. Crystallogr., 55, 1432-1443. (Pubitemid 29395738)
35. Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J. et al. (2012) The Pfam protein families database. Nucleic Acids Res., 40, D290-D301.
36. Yang, W. (2011) Nucleases: diversity of structure, function and mechanism. Q Rev. Biophys., 44, 1-93.
37. Yang, W. (2008) An equivalent metal ion in one-and two-metal-ion catalysis. Nat. Struct. Mol. Biol., 15, 1228-1231.
38. Dupureur, C.M. (2010) One is enough: insights into the two-metal ion nuclease mechanism from global analysis and computational studies. Metallomics, 2, 609-620.
39. Liang, J., Saad, Y., Lei, T., Wang, J., Qi, D., Yang, Q., Kolattukudy, P.E. and Fu, M. (2010) MCP-induced protein 1 deubiquitinates TRAF proteins and negatively regulates JNK and NF-kappaB signaling. J. Exp. Med., 207, 2959-2973.