3UI3
Structural and Biochemical Characterization of HP0315 from Helicobacter pylori as a VapD Protein with an Endoribonuclease Activity
Summary for 3UI3
| Entry DOI | 10.2210/pdb3ui3/pdb |
| Descriptor | Immunoglobulin G-binding protein G, Virulence-associated protein D (2 entities in total) |
| Functional Keywords | ferrodoxin-like fold, virulence associated protein d, ribonuclease, rna binding protein |
| Biological source | Streptococcus More |
| Total number of polymer chains | 2 |
| Total formula weight | 37445.18 |
| Authors | Kwon, A.R.,Kim, J.H.,Lee, B.J. (deposition date: 2011-11-04, release date: 2012-02-08, Last modification date: 2024-11-13) |
| Primary citation | Kwon, A.R.,Kim, J.H.,Park, S.J.,Lee, K.Y.,Min, Y.H.,Im, H.,Lee, I.,Lee, K.Y.,Lee, B.J. Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity. Nucleic Acids Res., 2012 Cited by PubMed Abstract: VapD-like virulence-associated proteins have been found in many organisms, but little is known about this protein family including the 3D structure of these proteins. Recently, a relationship between the Cas2 family of ribonucleases associated with the CRISPR system of microbial immunity and VapD was suggested. Here, we show for the first time the structure of a member of the VapD family and present a relationship of VapD with Cas2 family and toxin-antitoxin (TA) systems. The crystal structure of HP0315 from Helicobacter pylori was solved at a resolution of 2.8 Å. The structure of HP0315, which has a modified ferredoxin-like fold, is very similar to that of the Cas2 family. Like Cas2 proteins, HP0315 shows endoribonuclease activity. HP0315-cleaved mRNA, mainly before A and G nucleotides preferentially, which means that HP0315 has purine-specific endoribonuclease activity. Mutagenesis studies of HP0315 revealed that D7, L13, S43 and D76 residues are important for RNase activity, in contrast, to the Cas2 family. HP0315 is arranged as an operon with HP0316, which was found to be an antitoxin-related protein. However, HP0315 is not a component of the TA system. Thus, HP0315 may be an evolutionary intermediate which does not belong to either the Cas2 family or TA system. PubMed: 22241770DOI: 10.1093/nar/gkr1305 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.8 Å) |
Structure validation
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