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Systematic investigation of sequence and structural motifs that recognize ATP

Paper ID Volume ID Publish Year Pages File Format Full-Text
15064 1370 2015 11 PDF Available
Title
Systematic investigation of sequence and structural motifs that recognize ATP
Abstract

•Five ATP–protein interaction binding modes are discovered.•Sequence motifs are refined for two known motifs and identified for three novel motifs.•A method is developed to identify structurally conserved residues and structural motifs.

Interaction between ATP, a multifunctional and ubiquitous nucleotide, and proteins initializes phosphorylation, polypeptide synthesis and ATP hydrolysis which supplies energy for metabolism. However, current knowledge concerning the mechanisms through which ATP is recognized by proteins is incomplete, scattered, and inaccurate. We systemically investigate sequence and structural motifs of proteins that recognize ATP. We identified three novel motifs and refined the known p-loop and class II aminoacyl-tRNA synthetase motifs. The five motifs define five distinct ATP–protein interaction modes which concern over 5% of known protein structures. We demonstrate that although these motifs share a common GXG tripeptide they recognize ATP through different functional groups. The p-loop motif recognizes ATP through phosphates, class II aminoacyl-tRNA synthetase motif targets adenosine and the other three motifs recognize both phosphates and adenosine. We show that some motifs are shared by different enzyme types. Statistical tests demonstrate that the five sequence motifs are significantly associated with the nucleotide binding proteins. Large-scale test on PDB reveals that about 98% of proteins that include one of the structural motifs are confirmed to bind ATP.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slide(A) Superimposed cluster of ATP-binding site structures that belong to the “class II aminoacyl- tRNA synthetase” binding mode. (B) Structural motif identified by a clustering method for the “class II aminoacyl- tRNA synthetase” binding mode.

Keywords
ATP; Binding site; Sequence motif; Structural motif
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Systematic investigation of sequence and structural motifs that recognize ATP
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 56, June 2015, Pages 131–141
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us