NMR solution structure of HP0827 (O25501_HELPY) from Helicobacter pylori: model of the possible RNA-binding site.
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, beta1-alpha1-beta2-beta3-alpha2-beta4 (alpha; alpha-helix and beta; beta-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 beta sheets of HP0827, especially beta1 and beta3, 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 alpha1-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.
Jang
Sun-Bok
SB
Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, San 56-1, Shillim-Dong, Kwanak-Gu, Seoul 151-742, Korea.
Ma
Chao
C
Lee
Ji-Yoon
JY
Kim
Ji-Hun
JH
Park
Sung Jean
SJ
Kwon
Ae-Ran
AR
Lee
Bong-Jin
BJ
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D002850:Chromatography, Gel; D002942:Circular Dichroism; D016480:Helicobacter pylori / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D012329:RNA, Bacterial / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012996:Solutions; D055672:Static Electricity; D040681:Structural Homology, Protein; D013499:Surface Properties; D013696:Temperature; D013816:Thermodynamics
D001426:Bacterial Proteins; D012329:RNA, Bacterial; D016601:RNA-Binding Proteins; D012996:Solutions