On the importance of backbone loop and peptide flip in the Walker sequence in F1-ATPase action.
The Walker sequence, GXXXXGKT, present in all the six subunits of F1-ATPase exists in a folded form, known as phosphate-binding loop (P-loop). Analysis of the Ramachandran angles showed only small RMS deviation between the nucleotide-bound and nucleotide-free forms. This indicated a good overlap of the backbone loops. The catalytic beta-subunits (chains D, E and F) showed significant changes in the Ramachandran angles and the side chain torsion angles, but not the structural alpha-subunits (chains A, B and C). Most striking among these are the changes associated with Va1160 and Gly161 corresponding to a flip in the peptide unit between them when a nucleotide is bound (chains D or F compared to nucleotide-free chain E). The conformational analysis further revealed a hitherto unnoticed hydrogen bond between amide-N of the flipped Gly161 and terminal phosphate-O of the nucleotide. This assigns a role for this conserved amino acid, otherwise ignored, of making an unusual direct interaction between the peptide backbone of the enzyme protein and the incoming nucleotide substrate. Significance of this interaction is enhanced, as it is limited only to the catalytic subunits, and also likely to involve a mechanical rotation of bonds of the peptide unit. Hopefully this is part of the overall events that link the chemical hydrolysis of ATP with the mechanical rotation of this molecule, now famous as tiny molecular motor.
Department of Biochemistry, Indian Institute of Science, Bangalore 560 012. trs@biochem.iisc.ernet.in
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Ramasarma
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Ramakrishnan
D000255:Adenosine Triphosphate / Q000737:chemistry; D000577:Amides / Q000737:chemistry; D000595:Amino Acid Sequence; D001665:Binding Sites; D001671:Biochemistry / Q000379:methods; D002384:Catalysis; D020134:Catalytic Domain; D006860:Hydrogen Bonding; D006868:Hydrolysis; D008928:Mitochondria / Q000201:enzymology; D008956:Models, Chemical; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D006180:Proton-Translocating ATPases / Q000737:chemistry*
D000577:Amides; D010455:Peptides; D000255:Adenosine Triphosphate; D006180:Proton-Translocating ATPases