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By exploiting three-dimensional structure comparison, which is more sensitive than conventional sequence-based methods for detecting remote homology, we have identified a set of 140 ancestral protein domains using very restrictive criteria to minimize the potential error introduced by horizontal gene transfer. These domains are highly likely to have been(More)
The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43,229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds.(More)
The level of diadenosine 5',5"-P1-P4-tetraphosphate (diadenosine tetraphosphate or Ap4A), catecholamines, ATP and other nucleotides has been investigated in perchloric acid extracts of bovine adrenal medulla, chromaffin granules and cultured chromaffin cells. As a control, the amount of Ap4A and ATP has also been measured in human blood platelets. The(More)
Yeast (Saccharomyces cerevisiae) acetyl coenzyme A (CoA) synthetase (EC catalyzes the synthesis of adenosine 5'-tetraphosphate (P4A) and adenosine 5'-pentaphosphate (p5A) from ATP and tri- or tetrapolyphosphate (P3 or P4), with relative velocities of 7:1, respectively. Of 12 nucleotides tested as potential donors of nucleotidyl moiety, only ATP,(More)
Two enzymatic activities that split diadenosine triphosphate have been reported in Escherichia coli: a specific Mg-dependent bis(5'-adenosyl) triphosphatase (EC and the bis(5'-adenosyl) tetraphosphatase (EC In addition to the activities of these two enzymes, a different enzyme activity that hydrolyzes dinucleoside polyphosphates is(More)
The findings presented here originally arose from the suggestion that the synthesis of dinucleoside polyphosphates (Np(n)N) may be a general process involving enzyme ligases catalyzing the transfer of a nucleotidyl moiety via nucleotidyl-containing intermediates, with release of pyrophosphate. Within this context, the characteristics of the following(More)
DNA ligase from the hyperthermophilic marine archaeon Pyrococcus furiosus (Pfu DNA ligase) synthesizes adenosine 5′-tetraphosphate (p4A) and dinucleoside polyphosphates by displacement of the adenosine 5′-monophosphate (AMP) from the Pfu DNA ligase–AMP (E-AMP) complex with tripolyphosphate (P3), nucleoside triphosphates (NTP), or nucleoside diphosphates(More)
A program written in Visual Basic has been developed to calculate the isoelectric point of proteins and other macromolecules bearing acid-basic residues. The pI value can be theoretically calculated with the precision required. The computer automatically supplies a representation of the charge of the protein versus pH values. The corresponding values can(More)
Luciferase catalyzes the preferential synthesis of adenosine(5')tetraphospho(5')nucleoside (Ap4N) in the presence of luciferin (LH2), adenosine 5'-[gamma-thio]triphosphate (ATP[gamma S]) and NTP (other than ATP), with very low, or undetectable synthesis of Ap4A or Np4N, because ATP[gamma S] is a good adenylyl donor for the formation of the E-LH2-AMP(More)
T4 DNA ligase (EC, one of the most widely used enzymes in genetic engineering, transfers AMP from the E-AMP complex to tripolyphosphate, ADP, ATP, GTP or dATP producing p4A, Ap3A, Ap4A, Ap4G and Ap4dA, respectively. Nicked DNA competes very effectively with GTP for the synthesis of Ap4G and, conversely, tripolyphosphate (or GTP) inhibits the(More)