3V34

Crystal structure of MCPIP1 conserved domain with magnesium ion in the catalytic center

Summary for 3V34

• Entry DOI: 10.2210/pdb3v34/pdb
• Related: 3V32 3V33
• Descriptor: Ribonuclease ZC3H12A, MAGNESIUM ION (3 entities in total)
• Functional Keywords: rossmann-like sandwich fold, rnase, cytoplastic, hydrolase
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm (By similarity): Q5D1E8
• Total number of polymer chains: 2
• Total formula weight: 42627.22

Authors

Xu, J.,Peng, W.,Sun, Y.,Wang, X.,Xu, Y.,Li, X.,Gao, G.,Rao, Z. (deposition date: 2011-12-12, release date: 2012-05-23, Last modification date: 2024-03-20)

Primary citation

Xu, J.,Peng, W.,Sun, Y.,Wang, X.,Xu, Y.,Li, X.,Gao, G.,Rao, Z.
Structural study of MCPIP1 N-terminal conserved domain reveals a PIN-like RNase
Nucleic Acids Res., 40:6957-6965, 2012

PubMed Abstract: MCP-1-induced protein 1 (MCPIP1) plays an important role in the downregulation of the LPS-induced immune response by acting as an RNase targeting IL-6 and IL-12b mRNAs. A conserved domain located in the N-terminal part of MCPIP1 is thought to be responsible for its RNase activity, but its catalytic mechanism is not well understood due to the lack of an atomic resolution structure. We determined the 3D crystal structure of this MCPIP1 N-terminal conserved RNase domain at a resolution of 2.0 Å. The overall structure of MCPIP1 N-terminal conserved domain shares high structural homology with PilT N-terminal domain. We show that the RNase catalytic center is composed of several acidic residues, verifying their importance by site-specific mutagenesis. A positively charged arm close to the catalytic center may act as an RNA substrate-binding site, since exchange of critical positively charged residues on this arm with alanine partially abolish the RNase activity of MCPIP1 in vivo. Our structure of the MCPIP1 N-terminal conserved domain reveals the details of the catalytic center and provides a greater understanding of the RNA degradation mechanism.

PubMed: 22561375
DOI: 10.1093/nar/gks359

Experimental method

X-RAY DIFFRACTION (2.003 Å)