Here we identify the determinants of the nucleotide-binding ability associated with the P-loop-containing proteins, inferring their functional importance from their structural convergence to a unique three- dimensional (3D) motif. (1) A new surface 3D pattern is identified for the P-loop nucleotide-binding region, which is more selective than the corresponding sequence pattern; (2) the signature displays one residue that we propose is the determinant for the guanine-binding ability (the residues aligned to ras D119; this residue is known to be important only in the G-proteins, we extend the prediction to all the other P-loop- containing proteins); and (3) two cases of convergent evolution at the molecular level are highlighted in the analysis of the active site: the positive charge aligned to ras K117 and the arginine residues aligned to the GAP arginine finger. The analysis of the residues conserved on protein surfaces allows one to identify new functional or evolutionary relationships among protein structures that would not be detectable by conventional sequence or structure comparison methods.

Via, A., Ferrè, F., Brannetti, B., Valencia, A., HELMER CITTERICH, M. (2000). Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution. JOURNAL OF MOLECULAR BIOLOGY, 303(4), 455-465 [10.1006/jmbi.2000.4151].

Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution

HELMER CITTERICH, MANUELA
2000-11-03

Abstract

Here we identify the determinants of the nucleotide-binding ability associated with the P-loop-containing proteins, inferring their functional importance from their structural convergence to a unique three- dimensional (3D) motif. (1) A new surface 3D pattern is identified for the P-loop nucleotide-binding region, which is more selective than the corresponding sequence pattern; (2) the signature displays one residue that we propose is the determinant for the guanine-binding ability (the residues aligned to ras D119; this residue is known to be important only in the G-proteins, we extend the prediction to all the other P-loop- containing proteins); and (3) two cases of convergent evolution at the molecular level are highlighted in the analysis of the active site: the positive charge aligned to ras K117 and the arginine residues aligned to the GAP arginine finger. The analysis of the residues conserved on protein surfaces allows one to identify new functional or evolutionary relationships among protein structures that would not be detectable by conventional sequence or structure comparison methods.
3-nov-2000
Pubblicato
Rilevanza internazionale
Articolo
Sì, ma tipo non specificato
Settore BIO/11 - BIOLOGIA MOLECOLARE
English
Con Impact Factor ISI
Protein Structure, Tertiary; Evolution, Molecular; Nucleoside-Phosphate Kinase; Conserved Sequence; Amino Acid Motifs; Adenosine Triphosphate; Static Electricity; Ribonucleases; Animals; Arginine; Binding Sites; Humans; Models, Molecular; Alanine; Substrate Specificity; Guanosine Triphosphate; GTP-Binding Proteins; Molecular Sequence Data; Sequence Alignment; Asparagine; Amino Acid Sequence
Via, A., Ferrè, F., Brannetti, B., Valencia, A., HELMER CITTERICH, M. (2000). Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution. JOURNAL OF MOLECULAR BIOLOGY, 303(4), 455-465 [10.1006/jmbi.2000.4151].
Via, A; Ferrè, F; Brannetti, B; Valencia, A; HELMER CITTERICH, M
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2108/15495
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