Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:6.3.5.5 (CPS)
 1,262 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Interdomain interactions play an important role in the structural organization of many enzymes and the conformational flexibility of their molecules. In this review, the role of intrasubunit and intersubunit domain-domain interactions in the origins of pre-existent asymmetry of homo-oligomeric D-glyceraldehyde-3-phosphate dehydrogenase and tryptophanyl-tRNA synthetase is discussed on the basis of recent X-ray data and other available information about the properties of these and related enzymes. In addition, a novel key function of interdomain interactions is considered: their potential contribution to intramolecular channeling of intermediates between active centers located on different subunits of a hetero-oligomeric enzyme (alpha,beta-heterodimeric carbamoyl phosphate synthetase).
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PMID:Interdomain interactions in oligomeric enzymes: creation of asymmetry in homo-oligomers and role in metabolite channeling between active centers of hetero-oligomers. 1116 53

A novel protein structure alignment technique has been developed reducing much of the secondary and tertiary structure to a sequential representation greatly accelerating many structural computations, including alignment. Constructed from incidence relations in the Delaunay tetrahedralization, alignments of the sequential representation describe structural similarities that cannot be expressed with rigid-body superposition and complement existing techniques minimizing root-mean-squared distance through superposition. Restricting to the largest substructure superimposable by a single rigid-body transformation determines an alignment suitable for root-mean-squared distance comparisons and visualization. Restricted alignments of a test set of histones and histone-like proteins determined superpositions nearly identical to those produced by the established structure alignment routines of DaliLite and ProSup. Alignment of three, increasingly complex proteins: ferredoxin, cytidine deaminase, and carbamoyl phosphate synthetase, to themselves, demonstrated previously identified regions of self-similarity. All-against-all similarity index comparisons performed on a test set of 45 class I and class II aminoacyl-tRNA synthetases closely reproduced the results of established distance matrix methods while requiring 1/16 the time. Principal component analysis of pairwise tetrahedral decomposition similarity of 2300 molecular dynamics snapshots of tryptophanyl-tRNA synthetase revealed discrete microstates within the trajectory consistent with experimental results. The method produces results with sufficient efficiency for large-scale multiple structure alignment and is well suited to genomic and evolutionary investigations where no geometric model of similarity is known a priori.
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PMID:Structure alignment via Delaunay tetrahedralization. 1585 81