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Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity.

Kwon AR, Kim JH, Park SJ, Lee KY, Min YH, Im H, Lee I, Lee KY, Lee BJ - Nucleic Acids Res. (2012)

Bottom Line: 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.HP0315 is arranged as an operon with HP0316, which was found to be an antitoxin-related protein.Thus, HP0315 may be an evolutionary intermediate which does not belong to either the Cas2 family or TA system.

View Article: PubMed Central - PubMed

Affiliation: Department of Herbal Skin Care, College of Herbal Bio-Industry, Daegu Haany University, Gyeongsan 712-715, Korea.

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.

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Structural analysis according to α carbon B-factor. (A) The distribution of α carbon B-factor of each residues. The regions with high α carbon B-factor are colored under red. (B) High distribution of α carbon B-factor is represented with red color on the cartoon structure of HP0315.
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gkr1305-F2: Structural analysis according to α carbon B-factor. (A) The distribution of α carbon B-factor of each residues. The regions with high α carbon B-factor are colored under red. (B) High distribution of α carbon B-factor is represented with red color on the cartoon structure of HP0315.

Mentions: Figure 2A shows the distribution of the α carbon B-factor of the A molecule in the HP0315. High B-factor regions are located on α1 helix, the loop between β2 and β3 strands, the loop between β3 strand and α2 helix, and the C terminal tail (Figure 2B).Figure 2.


Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity.

Kwon AR, Kim JH, Park SJ, Lee KY, Min YH, Im H, Lee I, Lee KY, Lee BJ - Nucleic Acids Res. (2012)

Structural analysis according to α carbon B-factor. (A) The distribution of α carbon B-factor of each residues. The regions with high α carbon B-factor are colored under red. (B) High distribution of α carbon B-factor is represented with red color on the cartoon structure of HP0315.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351183&req=5

gkr1305-F2: Structural analysis according to α carbon B-factor. (A) The distribution of α carbon B-factor of each residues. The regions with high α carbon B-factor are colored under red. (B) High distribution of α carbon B-factor is represented with red color on the cartoon structure of HP0315.
Mentions: Figure 2A shows the distribution of the α carbon B-factor of the A molecule in the HP0315. High B-factor regions are located on α1 helix, the loop between β2 and β3 strands, the loop between β3 strand and α2 helix, and the C terminal tail (Figure 2B).Figure 2.

Bottom Line: 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.HP0315 is arranged as an operon with HP0316, which was found to be an antitoxin-related protein.Thus, HP0315 may be an evolutionary intermediate which does not belong to either the Cas2 family or TA system.

View Article: PubMed Central - PubMed

Affiliation: Department of Herbal Skin Care, College of Herbal Bio-Industry, Daegu Haany University, Gyeongsan 712-715, Korea.

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.

Show MeSH