An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins.
TLDR
A common evolutionary origin for all of the proteins in this class is proposed, and a pattern of amino acid properties required at each position is defined, which significantly matches sugar kinases, such as fuco-, glucono-, xylulo-, ribulo-, and glycerokinase.Abstract:
The functionally diverse actin, hexokinase, and hsp70 protein families have in common an ATPase domain of known three-dimensional structure. Optimal superposition of the three structures and alignment of many sequences in each of the three families has revealed a set of common conserved residues, distributed in five sequence motifs, which are involved in ATP binding and in a putative interdomain hinge. From the multiple sequence alignment in these motifs a pattern of amino acid properties required at each position is defined. The discriminatory power of the pattern is in part due to the use of several known three-dimensional structures and many sequences and in part to the "property" method of generalizing from observed amino acid frequencies to amino acid fitness at each sequence position. A sequence data base search with the pattern significantly matches sugar kinases, such as fuco-, glucono-, xylulo-, ribulo-, and glycerokinase, as well as the prokaryotic cell cycle proteins MreB, FtsA, and StbA. These are predicted to have subdomains with the same tertiary structure as the ATPase subdomains Ia and IIa of hexokinase, actin, and Hsc70, a very similar ATP binding pocket, and the capacity for interdomain hinge motion accompanying functional state changes. A common evolutionary origin for all of the proteins in this class is proposed.read more
Citations
More filters
Journal ArticleDOI
Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment
Charles E. Lawrence,Stephen F. Altschul,Mark S. Boguski,Jun Liu,Andrew F. Neuwald,John C. Wootton +5 more
TL;DR: A mathematical definition of this "local multiple alignment" problem suitable for full computer automation has been used to develop a new and sensitive algorithm, based on the statistical method of iterative sampling, that finds an optimized local alignment model for N sequences in N-linear time, requiring only seconds on current workstations.
Journal ArticleDOI
The P450 superfamily: update on new sequences, gene mapping, accession numbers, early trivial names of enzymes, and nomenclature.
David R. Nelson,Tetsuya Kamataki,David J. Waxman,F P Guengerich,Ronald W. Estabrook,René Feyereisen,Frank J. Gonzalez,Minor J. Coon,Irwin C. Gunsalus,Osamu Gotoh +9 more
TL;DR: The likelihood that this ancient gene superfamily has existed for more than 3.5 billion years, and that the rate of P450 gene evolution appears to be quite nonlinear, is discussed.
Journal ArticleDOI
Actin Binding Proteins: Regulation of Cytoskeletal Microfilaments
C.G. dos Remedios,Deepak Chhabra,Murat Kekic,Irina Dedova,Masako Tsubakihara,Desiree A. Berry,Neil J. Nosworthy +6 more
TL;DR: Several ABPs that regulate actin-driven assembly, i.e., movement that is independent of motor proteins, are selected that represent a family of related proteins in nature and are widely distributed in nature.
Journal ArticleDOI
Actin structure and function.
TL;DR: Structures of G-actin and F-actIn are reviewed and some of the interactions that control the polymerization and disassembly of actin are discussed, which make actin a critical player in many cellular functions, ranging from cell motility and the maintenance of cell shape and polarity to the regulation of transcription.
Journal ArticleDOI
Control of Cell Shape in Bacteria: Helical, Actin-like Filaments in Bacillus subtilis
TL;DR: The distribution of the proteins in different species of bacteria, and the similarity of their sequence to eukaryotic actins, suggest that the MreB-like proteins have a cytoskeletal, actin-like role in bacterial cell morphogenesis.
References
More filters
Journal ArticleDOI
Protein folding in the cell.
TL;DR: Folding and assembly of polypeptides in vivo involves other proteins, many of which belong to families that have been highly conserved during evolution.
PatentDOI
Method to identify protein sequences that fold into a known three-dimensional structure
TL;DR: In this article, a computer-assisted method for identifying protein sequences that fold into a known 3D structure was proposed, based on three key features of each residue's environment within the structure: (1) the total area of the residue's side-chain that is buried by other protein atoms, inaccessible to solvent; (2) the fraction of the side-chains area that is covered by polar atoms (O, N) or water; and (3) the local secondary structure.
Journal ArticleDOI
Atomic structure of the actin:DNase I complex.
TL;DR: The atomic models of the complex between rabbit skeletal muscle actin and bovine pancreatic deoxyribonuclease I both in the ATP and ADP forms have been determined byo X-ray analysis at an effective resolution of 2.8 Å and 3 Å.
Journal ArticleDOI
Database of homology-derived protein structures and the structural meaning of sequence alignment.
Chris Sander,Reinhard Schneider +1 more
TL;DR: A database of homology‐derived secondary structure of proteins (HSSP) is produced by aligning to each protein of known structure all sequences deemed homologous on the basis of the threshold curve, effectively increasing the number of known protein structures by a factor of five to more than 1800.
Journal ArticleDOI
Three-dimensional structure of the ATPase fragment of a 70K heat-shock cognate protein
TL;DR: Surprisingly, the nucleotide-binding 'core' of the ATPase fragment has a tertiary structure similar to that of hexokinase, although the remainder of the structures of the two proteins are completely dissimilar, suggesting that both the phosphotransferase mechanism and the substrate-induced conformational change intrinsic to the hexokinases may be used by the 70K heat shock-related proteins.