Journal of Biochemistry Advance Access originally published online on July 15, 2009
Journal of Biochemistry 2009 146(5):667-674; doi:10.1093/jb/mvp105
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NMR Solution Structure of HP0827 (O25501_HELPY) from Helicobacter pylori: Model of the Possible RNA-binding Site
1Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, San 56-1, Shillim-Dong, Kwanak-Gu, Seoul 151-742; and 2Department of Herbal Skin Care, College of Herbal Bio-Industry, Daegu Haany University, 290, Yugok-Dong, Gyeongsan-Si, Gyeongsangbuk-Do 712-715, Korea
*To whom correspondence should be addressed. Tel: +82-2-880-7869, Fax: +82-2-872-3632, E-mail: lbj{at}nmr.snu.ac.kr
Received June 1, 2009; Accepted July 6, 2009
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Abstract |
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The HP0827 protein is an 82-residue protein identified as a putative ss-DNA-binding protein 12RNP2 Precursor from Helicobacter pylori. Here, we have determined 3D structure of HP0827 using Nuclear Magnetic Resonance. It has a ferredoxin-like fold, β1–
1–β2–β3–2–β4 (; -helix and β; β-sheet) and ribonucleoprotein (RNP) motifs which are thought to be important in RNA binding. By using structural homologues search and analyzing electrostatic potential of surface, we could compared HP0827 with other RNA-binding proteins (sex-lethal, T-cell restricted intracellular antigen-1, U1A) to predict RNA-binding sites of HP0827. We could predict that β sheets of HP0827, especially β1 and β3, are primary region for RNA binding. Consequently, similar to other RNA-binding proteins, RNP motifs (Y5, F45, F47), positively charged and hydrophobic regions (K32, R37, K40, K41, K43, R70, R73) are proposed as a putative RNA-binding sites. In addition, differences in amino acids composition of RNP motifs, N, C-terminal residues, loop-region fold and the orientation of 1-helix with other RNA recognition motif proteins could give specific biological functions to HP0827. Finally, the study on natural RNA target is also important to completely understand the biological function of HP0827.
Key Words: Helicobacter pylori, HP0827, RNP motif, RRM, single-stranded DNA-binding proteins
Abbreviations: HP, Helicobacter pylori; RNP, ribonucleoprotein; RRM, RNA recognition motif; PABP, PolyA-binding protein; OD, optical density; NMR, Nuclear Magnetic Resonance; CD, circular dichroism; CSI, chemical shift index; NOESY, nuclear overhauser enhancement spectroscopy; TROSY, transverse relaxation optimized spectroscopy; PDB, protein data bank; TIA-1, T-cell-restricted intracellular antigen-1; UV, ultraviolet