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PubMed2000

Congenital and inherited polycythemia.

Absolute polycythemia is a condition with increased red blood cell mass. There are a number of primary and secondary polycythemic disorders leading to absolute polycythemia. Primary polycythemias are caused by a defect intrinsic to the erythroid progenitor cells. The best characterized primary polycythemia is the autosomal dominant primary familial and congenital polycythemia (PFCP). Familial or childhood occurrence of the myeloproliferative disorder polycythemia vera are also discussed, emphasizing the importance of distinction between polycythemia vera and PFCP. Congenital or familial secondary polycythemic conditions are characterized by increased red cell mass, which is caused by circulating serum factors, typically erythropoietin.

2,3-Diphosphoglycerate↗
PubMed1981

Analysis and predication of structural motifs in the glycolytic enzymes.

Protein crystallography has determined the three-dimensional structures of 10 of the 13 enzymes of the glycolytic pathway. Diagrams and details of these enzyme structures are given in the paper. Most of the enzyme domains are variations and extensions of a many (4--9)-stranded, predominantly or totally parallel, beta-sheet that is shielded from solvent by alpha-helices (i.e. alpha/beta structures). There are strong structural similarities between the domains of some, but not all, of the enzymes. In particular the dinucleotide binding fold of lactate dehydrogenase and the beta-barrel of triose phosphate isomerase are found in other domains. General rules governing the topology and packing of alpha-helices against a beta-sheet provide a basis for the combinatorial prediction of the tertiary fold of glycolytic domains from their amino acid sequence and observed secondary structure. The predication algorithm demonstrates that there are severe restrictions on the number of possible structures. However, these restrictions do not fully explain some of the remarkable structural similarities between different enzymes that probably result from evolution from a common ancestor.

Animals↗
PubMed1981

Pathological consequences of copper deficiency and cobalt deficiency.

Aspects of the pathology of copper deficiency in several species, and cobalt deficiency in sheep, are summarized. An attempt is made to interpret morphological changes in copper-deficient animals in terms of biochemical defects. The common denominator may be mitochondrial lesions, with a generalized effect on energy-dependent synthetic functions of the cell. In copper deficiency, such defects can be attributed to depletion of copper-dependent enzymes, while deficiency of cobalt in ruminants is, in effect, deficiency of vitamin B12. The pathological consequences of vitamin B12 deficiency form a syndrome, notable features of which are neurological and muscular lesions, in which the metabolic consequences of hepatic damage may play a significant role.

Anemia, Macrocytic↗
PubMed1979

The role of manganese in growth and sporulation of Bacillus subtilis.

Phosphoglycerate phosphomutase of Bacillus subtilis, Bacillus cereus and Bacillus megaterium required Mn2+ as cofactor, whereas the wheat germ and rabbit liver enzymes did not. In the absence of Mn2+, B. subtilis did not sporulate in normal sporulation media but it did sporulate if the proper ratio of glucose or glycerol and malate was used. Decoyinine, an inhibitor of guanosine monophosphate synthesis, induced sporulation in the presence of excess glucose and malate to the same extent with and without Mn2+. Apparently, phosphoglycerate phosphomutase is the only strictly Mn2+-requiring enzyme needed for optimal sporulation in normal sporulation media.

Adenosine↗
PubMed2002

A genetic algorithm for the identification of conformationally invariant regions in protein molecules.

Understanding macromolecular function often relies on the comparison of different structural models of a molecule. In such a comparative analysis, the identification of the part of the molecule that is conformationally invariant with respect to a set of conformers is a critical step, as the corresponding subset of atoms constitutes the reference for subsequent analysis for example by least-squares superposition. A method is presented that categorizes atoms in a molecule as either conformationally invariant or flexible by automatic analysis of an ensemble of conformers (e.g. crystal structures from different crystal forms or molecules related by non-crystallographic symmetry). Different levels of coordinate precision, both for different models and for individual atoms, are taken explicitly into account via a modified form of Cruickshank's DPI [Cruickshank (1999), Acta Cryst. D55, 583-601] and are propagated into error-scaled difference distance matrices [Schneider (2000), Acta Cryst. D56, 715-721]. All pairwise error-scaled difference distance matrices are then analysed simultaneously using a genetic algorithm. The algorithm has been tested on several well known examples and has been found to converge rapidly to reasonable results using a standard set of parameters. In addition to the description of the algorithm, a criterion is suggested for testing the identity of two three-dimensional models within experimental error without any explicit superposition.

Algorithms↗
PubMed1983

A further case of monosomy 10qter.

A child with a terminal deletion of chromosome 10 (q26) is described. A comparison of the phenotypic and cytogenetic features is made in the five reported cases of monosomy 10qter. No phenotypic features are found sufficiently characteristic to delineate a syndrome. Enzymatic activities for PGAMA and GOT1 were normal.

Aspartate Aminotransferases↗
PubMed2006

Current role of liver transplantation for methylmalonic acidemia: a review of the literature.

To evaluate the current role of liver transplantation (LT) for methylmalonic acidemia (MMA), we reviewed the literature on outcomes of this treatment, and describe three of our own cases of living-donor liver transplantation (LDLT). The total number of LT cases identified was 18. Transplantation mode was deceased donor LT in 12, including five combined liver-kidney transplantations (CLKT) from deceased donors, and LDLT in six. Three hospital mortalities were noted, because of metabolic decompensation, sepsis and aspergillosis. Although mean postoperative serum MMA level decreased to 13.8% +/- 9.2% (range 1.25-26.1%) of preoperative levels, four patients (22.2%) had renal insufficiency after isolated LT and three (16.7%) had postoperative neurological disability. Continuing metabolic damage to the kidney and brain may occur even after successful LT. Further evaluation is required to determine the long-term suitability of this treatment modality.

Adolescent↗
PubMed1984

31P NMR spin-transfer in the phosphoglyceromutase reaction.

The rate of exchange of phosphoryl groups between 2- and 3-phosphoglycerate catalysed by (a) high concentrations (approximately equal to 5.0 mg protein ml-1) of rabbit muscle phosphoglyceromutase and (b) lysed human erythrocytes was measured using saturation and inversion transfer techniques with 31P-NMR spectroscopy. This is the first reported application of these techniques to a study of this particular enzymic reaction either in vitro or in situ in a cell cytosol. Selective irradiation of resonances was achieved by the DANTE pulse sequence which had not previously been used for spin-transfer studies. New equilibrium exchange theory was developed for the simplest model of a two-reactant enzyme-catalysed reaction and this was used to calculate turnover rates for the enzymes. There was a close similarity between the turnover rates calculated from the spin-transfer data obtained from the systems in vitro and in situ and those obtained by conventional enzymic assays, at low enzyme concentrations. This suggested an absence of any homogeneous enzyme-enzyme interactions which modify the kinetics at high protein concentrations either in lysates or in the system in vitro.

Animals↗
PubMed1994

A method for increasing the concentration of a specific internal metabolite in steady-state systems.

An approach is described by which it is possible to increase the concentration of any internal metabolite without affecting the concentrations of other metabolites and fluxes in the organism. This approach requires the manipulation of only a limited number of enzyme activities. The method shows which enzymes to manipulate and the extent of the manipulation required to achieve a given increase in a chosen metabolite. A case study involving tryptophan overproduction in Saccharomyces cerevisae is given as a practical example of how this method could be used.

3-Deoxy-7-Phosphoheptulonate Synthase↗
PubMed1995

Histidine residues 139, 363 and 500 are essential for catalytic activity of cofactor-independent phosphoglyceromutase from developing endosperm of the castor plant.

Cofactor-independent phosphoglyceromutase (PGM) from castor is inactivated by diethyl pyrocarbonate, implicating histidine residues in the catalytic mechanism. Treatment of the inhibited enzyme with 1 M hydroxylamine at pH 7.0 restores the enzyme activity. Spectroscopic data indicate that the inactivation of PGM with diethyl pyrocarbonate is the result of formation of carbethoxyhistidine derivatives. The substrate, 3-phosphoglycerate, substantially protects the enzyme against diethyl pyrocarbonate inactivation, indicating that the histidine residues important in catalysis are at or near the active site of the enzyme. There are 12 conserved histidine residues in all plant PGMs that have been sequenced. In the castor PGM, these conserved histidine residues were changed to either valine (H12V) or alanine (H41A, H65A, H84A, H127A, H139A, H163A, H363A H433A, H471A, H500A and H540A) by in vitro mutagenesis. Expression of these mutant proteins in Escherichia coli produced seven soluble mutant proteins (mutations H41A, H65A, H84A, H139A, H363A, H500A and H540A) and five insoluble mutant proteins (mutations H12V, H127A, H163A, H433A and H471A). Among the seven soluble proteins, four possessed normal PGM activity (mutations H41A, H65A, H84A and H540A) and three (mutations H139A, H363A and H500A) had no catalytic activity. Along with the in-vitro-expressed wild-type enzyme, mutant enzymes [H139A]PGM, [H363A]PGM and [H500A]PGM were purified to homogeneity. Purified wild-type PGM expressed in E. coli was active and had a Km value very close to that of the enzyme purified from castor endosperm, while the three mutant enzymes remained inactive throughout purification. Therefore, histidine residues 139, 363 and 500 appear to be essential for the catalytic activity of the cofactor-independent enzyme, and may be located at the active site. Hence, although the cofactor-dependent and cofactor-independent PGMs have no homology in their primary amino acid sequences, both enzymes appear to utilize histidine residues to mediate the transfers of proton and phospho groups in the reaction, and thus may be functionally and mechanistically convergent.

Amino Acid Sequence↗
PubMed1997

The fructose transporter of Bacillus subtilis encoded by the lev operon: backbone assignment and secondary structure of the IIB(Lev) subunit.

The fructose transporter of the Bacillus subtilis phosphotransferase system consists of two membrane associated (IIA and IIB) and two transmembrane (IIC and IID) subunits [Martin-Verstraete, I., Débarbouille, M., Klier, A. & Rapoport, G. (1990) J. Mol. Biol. 214, 657-671] . It mediates uptake by a mechanism which couples translocation to phosphorylation of the transported solute. The 18-kDa IIBLev subunit transfers phosphoryl groups from His9 of the IIA subunit to the sugar. The three-dimensional structure of IIBLev or similar proteins is not known. IIBLev was overexpressed in Escherichia coli and isotopically labelled with 13C/15N in H2O as well as in 70% D2O. 15N-edited NOESY, 13C-edited NOESY and 13C,15N triple-resonance experiments yielded a nearly complete assignment of the 1H, 13C and 15N resonances. Based on qualitative interpretation of NOE, scalar couplings, chemical shift values and amide exchange data, the secondary structure and topology of IIBLev was determined. IIBLev comprises six parallel beta-strands, one antiparallel beta-strand and 5 alpha-helices. The order of the major secondary-structure elements is (beta alpha)5beta (strand order 7651423). Assuming that the (beta alpha beta)-motives form right-handed turn structures, helices alphaA and alphaB are packed to one face and helices alphaC, alphaD and alphaE to the opposite face of the parallel beta-sheet. His15 which is transiently phosphorylated during catalysis is located in the loop beta1/alphaA of the topological switch point. The amino terminal (beta/alpha)4 part of IIBLev has the same topology as phosphoglyceromutase (PGM; PDB entry 3pgm). Both proteins catalyze phosphoryltransfer reactions which proceed through phosphohistidine intermediates and they show a similar distribution of invariant residues in the topologically equivalent positions of their active sites. The protein fold of IIBLev has no similarity to any of the known structures of other phosphoenolpyruvate-dependent-carbohydrate-phosphotransferase-system proteins.

Amino Acid Sequence↗
PubMed1980

Changes in the activity and isozyme patterns of glycolytic enzymes during stimulation of normal human lymphocytes with phytohaemagglutinin.

A study has been made of the effects of phytohaemagglutinin on the gene expression of the glycolytic enzymes in cultured human lymphocytes. All the enzymes were found to show an average increase in activity of between 160% and 360% in stimulated cells, but the increases were greater for the enzymes comprising the second half of the pathway. The enzyme activities in stimulated cells, cultured for 72 h, were similar to the activities measured in long-term lymphoid lines. Starch-gel electrophoresis was used to examine the isozyme patterns of the enzymes before and after exposure of the lymphocytes to PHA. Six of the enzymes showed isozyme patterns unchanged by stimulation. Four of the enzymes, aldolase, triosephosphate isomerase, enolase and lactate dehydrogenase, showed different isozyme patterns in stimulated cells from those seen in uncultured or unstimulated cells. The electrophoretic results showed a good correlation in isozyme pattern between uncultured lymphocytes and cultured unstimulated lymphocytes, and between PHA-stimulated lymphocytes and long-term lymphoid lines.

Cells, Cultured↗
PubMed2000

A consensus Porphyromonas gingivalis promoter sequence.

We have determined the transcription start points (tsp) for recently identified Porphyromonas gingivalis W50 genes, kgp, rgpA, rgpB (formerly designated prtK, prtR, and prtRII respectively), fetB and the mcmAB operon. Alignment of the DNA upstream of these tsp and those from the literature has enabled us to identify consensus sequences that may represent a P. gingivalis promoter. There is a potential -10 hexamer sequence, 5'-TATATT-3' centred on average at -10/11 nt which is repeated at -19/20 nt and an upstream consensus, 5'-CAGAT(A/G)-3' which is centred at -39/40 nt.

Bacterial Outer Membrane Proteins↗