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At least 1,531 records · Page 85Linked to original sources
PubMed1992

Immunocytochemical localization of glycolytic and fermentative enzymes in Zymomonas mobilis.

Gold-labeled antibodies were used to examine the subcellular locations of 11 glycolytic and fermentative enzymes in Zymomonas mobilis. Glucose-fructose oxidoreductase was clearly localized in the periplasmic region. Phosphogluconate lactonase and alcohol dehydrogenase I were concentrated in the cytoplasm near the plasma membrane. The eight remaining enzymes were more evenly distributed within the cytoplasmic matrix. Selected enzyme pairs were labeled on opposite sides of the same thin section to examine the frequency of colocalization. Results from these experiments provide evidence that glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, and alcohol dehydrogenase I form an enzyme complex.

Alcohol Dehydrogenase↗
PubMed1983

Hereditary disorders of red cell enzymes in the Embden-Meyerhof pathway.

Recent advances about hereditary disorders of red cell enzymes in the Embden-Meyerhof glycolytic pathway and Rapoport-Leubering cycle are discussed with a stress on pyruvate kinase deficiency, because it is the most common and most intensively studied disorder among them. Broad genetic heterogeneity exists in all the known erythroenzymopathies. Recently, the primary structure of normal human red cell phosphoglycerate kinase has been determined and single amino acid substitutions of four mutant phosphoglycerate kinases have been clarified by Yoshida et al. These studies allowed analysis of structure-function relationships at the molecular level to be carried out more precisely than was previously possible. It is the consensus of the investigators working in this field that the pathogenesis in three-quarters of the congenital nonspherocytic hemolytic anemia patients remains unknown even after adequate red cell enzyme studies and isopropanol test for unstable hemoglobin have been done. This simply means that much studies remain to be worked out in this field.

Anemia, Hemolytic, Congenital↗
PubMed1980

Studies on the urinary acidic metabolites from three patients with methylmalonic aciduria.

By gas chromatographic mass spectrometric analysis, 2-methyl-3-oxovaleric acid, 3-oxovaleric acid, 3-hydroxyvaleric acid and 2-methyl-3-hydroxybutyric acid were identified in the urine from three patients with methylmalonic aciduria. The level of 2-methyl-3-oxovaleric acid increased with the increase of methylmalonic acid concentration and the level of 3-oxovaleric acid increased with the increase of ketone bodies. It was demonstrated that these metabolites are detectable from patients with propionic acidemia and methylmalonic aciduria when propionyl CoA accumulates in the cells of the patients either primarily or secondarily.

Carboxylic Acids↗
PubMed1984

Synthesis and levels of organic phosphates in erythrocytes during avian development: specific formation of BPG and IP5 in two distinct populations from young chicks.

Two generations of red cells (embryonic and definitive), different types of haemoglobins, and special organic phosphates involved in the control of haemoglobin oxygenation (2:3-bisphosphoglycerate, BPG, and inositol-5-phosphate, IP5), have been found progressively during development of the chick. Levels of both organic phosphates, as well as activities of the enzymes involved in BPG synthesis (2:3-bisphosphoglycerate synthase, BPGM) and IP5 formation (phytase), were studied in the erythrocyte populations from embryo, young and adult chickens. Measurement of specific activities of BPGM and phytase in the two subpopulations present in young chickens showed that these phosphates could be specifically and predominantly formed in these two red cell populations.

6-Phytase↗
PubMed1995

An enzyme in yeast mitochondria that catalyzes a step in branched-chain amino acid biosynthesis also functions in mitochondrial DNA stability.

The yeast mitochondrial high mobility group protein Abf2p is required, under certain growth conditions, for the maintenance of wild-type (rho+) mitochondrial DNA (mtDNA). We have identified a multicopy suppressor of the mtDNA instability phenotype of cells with a null allele of the ABF2 gene (delta abf2). The suppressor is a known gene, ILV5, encoding the mitochondrial protein, acetohydroxy acid reductoisomerase, which catalyzes a step in branched-chain amino acid biosynthesis. Efficient suppression occurs with just a 2- to 3-fold increase in ILV5 copy number. Moreover, in delta abf2 cells with a single copy of ILV5, changes in mtDNA stability correlate directly with changes in conditions that are known to affect ILV5 expression. Wild-type mtDNA is unstable in cells with an ILV5 null mutation (delta ilv5), leading to the production of mostly rho- petite mutants. The instability of rho+ mtDNA in delta ilv5 cells is not simply a consequence of a block in branched-chain amino acid biosynthesis, since mtDNA is stable in cells with a null allele of the ILV2 gene, which encodes another enzyme of that pathway. The most severe instability of rho+ mtDNA is observed in cells with null alleles of both ABF2 and ILV5. We suggest that ILV5 encodes a bifunctional protein required for branched-chain amino acid biosynthesis and for the maintenance of rho+ mtDNA.

2-Acetolactate Mutase↗
PubMed2005

Structural classification of thioredoxin-like fold proteins.

Protein structure classification is necessary to comprehend the rapidly growing structural data for better understanding of protein evolution and sequence-structure-function relationships. Thioredoxins are important proteins that ubiquitously regulate cellular redox status and various other crucial functions. We define the thioredoxin-like fold using the structure consensus of thioredoxin homologs and consider all circular permutations of the fold. The search for thioredoxin-like fold proteins in the PDB database identified 723 protein domains. These domains are grouped into eleven evolutionary families based on combined sequence, structural, and functional evidence. Analysis of the protein-ligand structure complexes reveals two major active site locations for the thioredoxin-like proteins. Comparison to existing structure classifications reveals that our thioredoxin-like fold group is broader and more inclusive, unifying proteins from five SCOP folds, five CATH topologies and seven DALI domain dictionary globular folding topologies. Considering these structurally similar domains together sheds new light on the relationships between sequence, structure, function and evolution of thioredoxins.

Amino Acid Motifs↗
PubMed1993

Improved calculations of compactness and a reevaluation of continuous compact units.

A new method for calculating compactness (Z) that uses look-up table-based algorithms for area and volume computations is introduced. These algorithms can be used in any iterative area or volume calculation, are more than 1000 times faster than the original algorithms, and have equal or better precision. With the faster algorithms it is now possible to calculate the compactness of all continuous units in a protein, and to precisely locate the optimal compact units without the screening functions and limited resolution used previously. These methods have been incorporated into a fully automatic domain finding algorithm, and this method has been applied to the 21 proteins originally analyzed as well as 12 additional proteins. This method is robust, and yields similar units even when applied to coordinates of protein crystals grown under different experimental conditions.

Alcohol Dehydrogenase↗
PubMed1995

Sequencing analysis of a 24.7 kb fragment of yeast chromosome XIV identifies six known genes, a new member of the hexose transporter family and ten new open reading frames.

The DNA sequence of a 24.7 kb region covering the left arm of chromosome XIV from Saccharomyces cerevisiae was determined. This region contains 17 open reading frames (ORFs) which code for proteins of more than 100 amino acids. Five ORFs correspond to the KRE1, ATP11, DAL82, RFA2 and MCK1 loci, described previously. Two ORFs present high similarity to known proteins: NO345 with the hexose transporter family, and NO351 with the yeast chorismate mutase/prephenate dehydratase enzyme encoded by PHA2. Six ORFs show limited similarity with known proteins or some specific features: NO339 presents 11 potential transmembrane domains. NO343, which is internal to NO345, presents a putative signal sequence and a potential transmembrane domain. NO348 shows similarity with YCW2, TUP1 and SEC13. NO364 reveals a signature for a pyridoxal-phosphate attachment site. Finally, NO384 and NO388 present a biased amino acid composition, being rich in Asn or Glu/Lys/Arg, respectively. Four other ORFs (NO342, NO376, NO381 and NO397) show no similarity to proteins within the databases screened.

Amino Acid Sequence↗
PubMed1994

Time-course curves of enzyme reactions with dilute substrates can be determined from the reverse reactions.

We present a novel and useful principle that can be applied to enzyme reactions with dilute substrates and enables to obtain the desired time-course curve from the reverse reaction when the latter can be measured more easily. Let us imagine an enzyme mixture that can catalyze the interconversion between substances A, B, C,.... If one substance (sufficiently dilute) is added to the mixture as the substrate and the time-course curve of the concentration of another substance is followed, then, "the time-course curve of A-->B" (which is the time-course curve of the concentration of substance B when substance A is added as the substrate) and that of the reverse reaction B-->A will coincide when plotted at appropriate scales of magnitude. Similar relation holds on any pair of substances even if they are widely separated in any type of reaction scheme. The principle was proved mathematically and holds on any first-order reaction network and can be applied on an enzyme reaction with a dilute substrate because it is reduced to a first-order reaction network. An example of experimental application of this principle is also given.

Catalysis↗
PubMed1995

Molecular structure of the Menkes disease gene (ATP7A).

We report a detailed molecular analysis of the genomic structure of the Menkes disease gene (MNK; ATP7A). There are 23 exons in ATP7A covering a genomic region of approximately 140 kb. The size of the individual coding exons varies between 77 and 726 bp, and introns vary in size between 196 bp and approximately 60 kb. All of the splice sites obey the consensus GT-AG rule except the splice donor of intron 9, which is GC instead of GT. The exon following this rare splice donor variant is alternatively spliced. A PGAM pseudogene and two highly polymorphic CA repeats map to introns within the gene. The structure is very similar to that of the closely related Wilson disease gene (WND; ATP7B). From exon 5 (exon 3 in ATP7B) to the end, all of the splice sites occur at exactly the same nucleotide positions as in the WND gene, except for the boundary between exons 17 and 18 (exons 15 and 16 in ATP7B) and a single codon difference at the boundary between exons 4 and 5 of the MNK gene (exons 2 and 3 in ATP7B). In contrast to the WND gene, in which the first four of six metal binding domains are contained in 1 exon, metal binding domains 1 to 4 are divided over 3 exons. The striking similarity of the MNK and WND genes at the genomic level is consistent with their relatively recent divergence from a common ancestral gene.

Adenosine Triphosphatases↗
PubMed1996

Deviations from standard atomic volumes as a quality measure for protein crystal structures.

Standard ranges of atomic and residue volumes are computed in 64 highly resolved and well-refined protein crystal structures using the classical Voronoi procedure. Deviations of the atomic volumes from the standard values, evaluated as the volume Z-scores, are used to assess the quality of protein crystal structures. To score a structure globally, we compute the volume Z-score root mean square deviation (Z-score rms), which measures the average magnitude of the volume irregularities in the structure. We find that the Z-score rms decreases as the resolution and R-factor improve, consistent with the fact that these improvements generally reflect more accurate models. From the Z-score rms distribution in structures with a given resolution or R-factor, we determine the normal limits in Z-score rms values for structures solved at that resolution or R-factor. Structures whose Z-score rms exceeds these limits are considered as outliers. Such structures also exhibit unusual stereochemistry, as revealed by other analyses. Absolute Z-scores of individual atoms are used to identify problems in specific regions within a protein model. These Z-scores correlate fairly well with the atomic B-factors, and atoms having absolute Z-scores > 3, occur at or near regions in the model where programs such as PROCHECK identify unusual stereochemistry. Atomic volumes, themselves not directly restrained in crystallographic refinement, can thus provide an independent, rather sensitive, measure of the quality of a protein structure. The volume-based structure validation procedures are implemented in the program PROVE (PROtein Volume Evaluation), which is accessible through the World Wide Web.

Amino Acid Sequence↗
PubMed2001

Mutation analysis of the MCM gene in Israeli patients with mut(0) disease.

Three novel mutations (IVS8+3a --> g, N219Y, and E414X) were identified in 6 unrelated patients with mut(0) methylmalonic aciduria. The presence of a wild-type along with rearranged fragments in homozygotes for the IVS8+3a --> g mutation may contribute to their later age of onset (3-11 months of age). Nonetheless, delayed onset was not associated with better neurological outcome and prolonged survival. The large number of undiagnosed dead sibs in most families suggests that the disease is largely underdiagnosed in this region.

Amino Acid Metabolism, Inborn Errors↗