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A conformational analysis of Walker motif A [GXXXXGKT (S)] in nucleotide-binding and other proteins

Ramakrishnan, C and Dani, VS and Ramasarma, T (2002) A conformational analysis of Walker motif A [GXXXXGKT (S)] in nucleotide-binding and other proteins. In: Protein Engineering, 15 (10). pp. 783-798.

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Abstract

The sequence GXXXXGKT/S, popularly known as Walker motif A, is widely believed to be the site for binding nucleotides in many proteins. Examination of the crystal structures in the Protein Data Bank showed that about half of the examples having these sequences do not bind or use nucleotides. Data analyses showed 92 different Walker sequences of the variable quartet (XXXX). Ramachandran angles in this segment revealed conformational similarity in the group of 45 proteins, known to bind or utilize nucleotides. The conformations of this segment in other proteins differ widely and it is not known whether they play any role in their functions. A flip of a peptide unit at different locations, with little change in the backbone conformation was noted in nine pairs of these proteins having same Walker sequence. An examination of the immediate neighborhood of the Walker sequence indicates that this region is preceded by a $\beta$-strand and followed by an $\alpha$-helix, resulting in the motif $\beta–W–\alpha$, an invariant feature amongst nucleotide-binding proteins.

Item Type: Journal Article
Additional Information: Copyright belongs to this article is Oxford University Press
Keywords: peptide flip;Ramachandran angles;beta turn;Walker motif
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Division of Biological Sciences > Biochemistry
Date Deposited: 11 Oct 2007
Last Modified: 19 Sep 2010 04:40
URI: http://eprints.iisc.ernet.in/id/eprint/12226

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