PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “enzyme evolution”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13Linked to original sources
PubMed2004

Structure and developmental expression of hatching enzyme genes of the Japanese eel Anguilla japonica: an aspect of the evolution of fish hatching enzyme gene.

We isolated seven cDNA clones from embryos of the Japanese eel Anguilla japonica. Each deduced amino acid sequence consisted of a signal peptide, a propeptide and a mature enzyme portion belonging to the astacin protease family. A phylogenetic analysis showed that the eel enzymes resembled the high choriolytic enzyme (HCE) of medaka Oryzias latipes, and the hatching enzymes of the zebra fish Danio rerio and masu salmon Oncorhynchus masou. Hatching enzymes of these teleosts belonged to the group of the medaka HCE, and not the medaka low choriolytic enzyme (LCE), another hatching enzyme of medaka. Southern blot analysis showed that the genes of the eel hatching enzymes were multicopy genes like the medaka HCE genes. However, one of the eel hatching enzyme genes comprised eight exons and seven introns, and the exon-intron organization was similar to the medaka LCE gene, which is a single-copy gene. The molecular evolution of the fish hatching enzyme genes is discussed. In addition, whole-mount in situ hybridization and immunocytochemistry showed that the eel hatching enzyme was first expressed in the pillow anterior to the forebrain of early neurula, and finally in the cell mass on the yolk sac of later stage embryos. The early differentiation profile of eel hatching gland cells was similar to that of medaka, masu salmon and zebrafish, whereas the final location of the gland cells was different among fishes.

Amino Acid Sequence↗
PubMed2002

Enzyme electrokinetics: hydrogen evolution and oxidation by Allochromatium vinosum [NiFe]-hydrogenase.

The mechanism of catalytic hydrogen evolution and oxidation by Allochromatium vinosum [NiFe]-hydrogenase has been studied by protein film voltammetry (PFV) with the enzyme adsorbed at a pyrolytic graphite edge electrode. By analyzing the entire shapes of catalytic voltammograms, the energetics of the catalytic cycles (reduction potentials and acidity constants of the active states), including the detailed profiles of activity against pH and the sequences of proton and electron transfers, have been determined, and these are discussed with respect to the mechanism. PFV, which probes rates as a continuous function of the electrochemical potential (i.e., in the "potential domain"), is proven to be an invaluable tool for determining the redox properties of an active site in the presence of its substrate, at room temperature, and during turnover. This is especially relevant in the case of the active states of hydrogenase, since one of its substrates (the proton) is always present at significant levels in the titration medium at physiological pH values.

Binding Sites↗
PubMed2002

Potassium- or sodium-efflux ATPase, a key enzyme in the evolution of fungi.

Potassium is the most abundant cation in cells. Therefore, plant-associated fungi and intracellular parasites are permanently or circumstantially exposed to high K(+) and must avoid excessive K(+) accumulation activating K(+) efflux systems. Because high K(+) and high pH are compatible in natural environments, free-living organisms cannot keep a permanent transmembrane DeltapH and cannot rely only on K(+)/H(+) antiporters, as do mitochondria. This study shows that the Schizosaccharomyces pombe CTA3 is a K(+)-efflux ATPase, and that other fungi are furnished with Na(+)-efflux ATPases, which also pump Na(+). All these fungal ATPases, including those pumping only Na(+), form a phylogenetic group, IID or ENA, among P-type ATPases. By searching in databases and partial cloning of ENA genes in species of Zygomycetes and Basidiomycetes, the authors conclude that probably all fungi have these genes. This study indicates that fungal K(+)- or Na(+)-ATPases evolved from an ancestral K(+)-ATPase, through processes of gene duplication. In yeast hemiascomycetes these duplications have occurred recently and produced bifunctional ATPases, whereas in Neurospora, and probably in other euascomycetes, they occurred earlier in evolution and produced specialized ATPases. In Schizosaccharomyces, adaptation to Na(+) did not involve the duplication of the K(+)-ATPase and thus it retains an enzyme which is probably close to the original one. The parasites Leishmania and Trypanosoma have ATPases phylogenetically related to fungal K(+)-ATPases, which are probably functional homologues of the fungal enzymes.

Adenosine Triphosphatases↗
PubMed1977

Kynureninase-type enzymes and the evolution of the aerobic tryptophan-to-nicotinamide adenine dinucleotide pathway.

Kynureninase-type (L-kynurenine hydrolase, EC 3.7.1.3) activity has been found to be present in the livers of fish, amphibia, reptiles, and birds. In addition to past information concerning this enzyme activity in mammalian liver, it is now clear that all the major classes of vertebrates carry a highly specialized kynureninase-type enzyme, which we have termed a hydroxykynureninase. To compare the reactivities of these enzymes with L-kynurenine and L-3-hydroxykynurenine, ratios of tau values (Km/V) were used. Based on this comparison, the bacterium Pseudomonas fluorescens carries the most efficient kynureninase, whereas the amphibian Xenopus laevis has the most efficient hydroxykynureniase. In these two cases, the ratio of tau values differs by a factor of 38 000. It is hypothesized that the tryptophan-to-nicotinamide adenine dinucleotide biosynthetic pathway evolved from a catabolic system of enzymes, and that the differences observed in the kynureninase-type enzymes between lower and higher organisms reflect the specialization of the function of these enzymes from a strictly catabolic role to an anabolic one during the course of evolution.

Animals↗
PubMed1998

Molecular analysis of phosphoglycerate kinase in Trypanoplasma borreli and the evolution of this enzyme in kinetoplastida.

In the protozoan kinetoplastid organism Trypanoplasma borreli, phosphoglycerate kinase (PGK) activity was found in two different cell compartments: 80% in the cytosol and 20% in peroxisome-like organelles called glycosomes. However, only one functional pgk gene could be detected, in addition to a pseudo-pgk gene. No short-range linkage could be established between these two genes, although they are presumably present on the same chromosome. The intact gene codes for a polypeptide of 411 amino acids, with a C-terminal extension of four residues, -VAKF, a sequence with probably a low targeting efficiency for glycosomes. The calculated net charge and molecular mass of the encoded polypeptide are +13 and 44230Da, respectively. In other Kinetoplastida, different tandemly arranged genes code for distinct PGK isoenzymes in glycosomes and cytosol. By comparison of the pgk gene organization, and a phylogenetic analysis, we have traced a plausible scenario of the evolution of the PGK isoenzymes in these organisms and of the enzymes' intracellular compartmentation.

Amino Acid Sequence↗
PubMed1987

Effect of vitamin E on the induction and evolution of enzyme-altered foci in the liver of rats treated with diethylnitrosamine.

The effects of dietary vitamin E (VE) on the steps of hepatocarcinogenesis, the induction and growth of gamma-glutamyltranspeptidase (GGT)-positive foci and their evolution into persistent nodules, were analyzed in the liver of rats treated with diethylnitrosamine (DEN). The induction of GGT-positive foci was inhibited by a diet containing 0.36-1.5% VE given after initiation with 200 mg/kg body weight (b.w.) DEN for 6 weeks with partial hepatectomy (PH) on week 3. The numbers and areas of GGT-positive foci were enhanced by diets containing 0.36 and 0.72% VE, given for 1 week after initiation with 10 mg/kg b.w. DEN and PH, followed by selection by 0.02% 2-acetylaminofluorene (AAF) and carbon tetrachloride (CCl4), but these were not enhanced by a diet containing 1.5% VE. Remodeling of hyperplastic nodules was not affected by the diet containing 0.72% VE given after initiation with DEN and selection for 12 weeks. The staining characteristics of GGT were different between remodeling and persistent nodules, except for those of the glutathione-S-transferase placental form (GST-P). The results obtained suggest that VE could prevent the very early events during hepatocarcinogenesis, the induction of phenotypically altered foci, but could no longer affect the later stages, the evolution of foci into persistent nodules.

Animals↗
PubMed2003

Evolution of an organophosphate-degrading enzyme: a comparison of natural and directed evolution.

Organophosphate-degrading enzyme from Agrobacterium radiobacter P230 (OPDA) is a recently discovered enzyme that degrades a broad range of organophosphates. It is very similar to OPH first isolated from Pseudomonas diminuta MG. Despite a high level of sequence identity, OPH and OPDA exhibit different substrate specificities. We report here the structure of OPDA and identify regions of the protein that are likely to give it a preference for substrates that have shorter alkyl substituents. Directed evolution was used to evolve a series of OPH mutants that had activities similar to those of OPDA. Mutants were selected for on the basis of their ability to degrade a number of substrates. The mutations tended to cluster in particular regions of the protein and in most cases, these regions were where OPH and OPDA had significant differences in their sequences.

Amino Acid Sequence↗
PubMed2003

Optimising enzyme function by directed evolution.

The past decade has seen a revolution in our ability to engineer designer enzymes using genetic tools that mimic evolution on a laboratory timescale. Many excellent examples of directed evolution applied to a wide range of enzymes have clearly demonstrated its future role in adapting enzymes for use in the chemical industry. Recent advances in 'smart' library design and computational screening are now permitting much deeper searches of sequence space, which potentially increases the extent to which enzyme function can be modified.

Animals↗
PubMed1991

Structural evolution of an enzyme specificity. The structure of rat carboxypeptidase A2 at 1.9-A resolution.

The structure of rat carboxypeptidase A2 (CPA2), which has a unique specificity for tryptophan-containing COOH-terminal peptides, has been determined in an unliganded state at 1.9-A resolution and refined to a crystallographic R-factor of 18.3%. Comparison of the structure of CPA2 with that of bovine carboxypeptidase A (referred to here as CPA1) reveals that the specificity of the former for larger amino acids probably arises from two amino acid replacements within the binding cavity (Thr268----Ala and Leu203----Met), coupled with differences in the positions of conserved residues in a surface loop on one face of the specificity pocket. The position of the reactive-site surface loop may be affected also by a disulfide bridge between Cys210 and Cys244. In this unliganded form of the enzyme, Tyr248 takes up a position interior to the specificity pocket and is distinct from that observed in bovine CPA1. The structural differences between CPA1 and CPA2 correlate strongly with crystallographically determined temperature factors and thus appear to be largest where the enzyme is flexible.

Amino Acid Sequence↗
PubMed2001

The AmiE aliphatic amidase and AmiF formamidase of Helicobacter pylori: natural evolution of two enzyme paralogues.

Aliphatic amidases (EC 3.5.1.4) are enzymes catalysing the hydrolysis of short-chain amides to produce ammonia and the corresponding organic acid. Such an amidase, AmiE, has been detected previously in Helicobacter pylori. Analysis of the complete H. pylori genome sequence revealed the existence of a duplicated amidase gene that we named amiF. The corresponding AmiF protein is 34% identical to its AmiE paralogue. Because gene duplication is widely considered to be a fundamental process in the acquisition of novel enzymatic functions, we decided to study and compare the functions of the paralogous amidases of H. pylori. AmiE and AmiF proteins were overproduced in Escherichia coli and purified by a two-step chromatographic procedure. The two H. pylori amidases could be distinguished by different biochemical characteristics such as optimum pH or temperature. AmiE hydrolysed propionamide, acetamide and acrylamide and had no activity with formamide. AmiF presented an unexpected substrate specificity: it only hydrolysed formamide. AmiF is thus the first formamidase (EC 3.5.1.49) related to aliphatic amidases to be described. Cys-165 in AmiE and Cys-166 in AmiF were identified as residues essential for catalysis of the corresponding enzymes. H. pylori strains carrying single and double mutations of amiE and amiF were constructed. The substrate specificities of these enzymes were confirmed in H. pylori. Production of AmiE and AmiF proteins is dependent on the activity of other enzymes involved in the nitrogen metabolism of H. pylori (urease and arginase respectively). Our results strongly suggest that (i) the H. pylori paralogous amidases have evolved to achieve enzymatic specialization after ancestral gene duplication; and (ii) the production of these enzymes is regulated to maintain intracellular nitrogen balance in H. pylori.

Amidohydrolases↗
PubMed1975

Origin and early evolution of transition element enzymes.

In this paper we speculate on the origin and early evolution of transition element enzymes. Iron, molybdenum, and zinc, the most abundant transition elements in seawater, presumably complexed with compounds accumulated in the primeval sea in the course of chemical evolution forming compounds with subsequently evolved to form proenzymes or early enzymes with low activity and broad specificity. Iron complexes may be regarded as precursors of electron transfer enzymes, molybdenum complexes as precursors of enzymes involved in the metabolism of small molecules, and zinc complexes as precursors of hydrolytic and transferring enzymes, including enzymes participating in the metabolism of macromolecules and information transfer. The different iron, molybdenum, and zinc enzymes found in bacteria including Clostridium may then have arisen through specialization by increases in the enzyme specificity of these proenzymes. Copper would have been incorporated as an enzyme constituent after the elevation of environmental redox potential, probably due to the accumulation of atmospheric oxygen.

Aerobiosis↗
PubMed2006

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution.

Pyridoxal kinase catalyses the phosphorylation of pyridoxal, pyridoxine and pyridoxamine to their 5' phosphates and plays an important role in the pyridoxal 5' phosphate salvage pathway. The crystal structure of a dimeric pyridoxal kinase from Bacillus subtilis has been solved in complex with ADP to 2.8 A resolution. Analysis of the structure suggests that binding of the nucleotide induces the ordering of two loops, which operate independently to close a flap on the active site. Comparisons with other ribokinase superfamily members reveal that B. subtilis pyridoxal kinase is more closely related in both sequence and structure to the family of HMPP kinases than to other pyridoxal kinases, suggesting that this structure represents the first for a novel family of "HMPP kinase-like" pyridoxal kinases. Moreover this further suggests that this enzyme activity has evolved independently on multiple occasions from within the ribokinase superfamily.

Adenosine Diphosphate↗
PubMedDate not supplied

A hybrid recognition sequence in a recombinant restriction enzyme and the evolution of DNA sequence specificity.

Early attempts to generate new restriction specificities by recombination between allelic restriction-modification systems have been unsuccessful. Bullas et al. succeeded in isolating a new specificity, SQ, in Salmonella that they interpreted as being the result of a recombination event between the parental strains, Salmonella typhimurium and S. postdam, which encode the SB and SP restriction systems, respectively. This interpretation has recently been confirmed by DNA heteroduplex studies with the SB, SP and SQ structural genes. We have determined the DNA sequences recognized by the SB and SP enzymes and found that, like all type I restriction sequences, they are split into two specific domains by a spacer of nonspecific sequence that, for both SB and SP, is 6 base pairs (bp) long. We have now determined the sequence recognized by the recombinant SQ enzyme and find that it is a hybrid between the SB and SP sequences, containing one specific domain from each parental strain. This result implies that each of the two specific domains is recognized by a physically distinct part of the enzyme.

Alleles↗