Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
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By means of neutron solution scattering we determined the position and orientation of core enzyme and sigma-factor within the Escherichia coli RNA polymerase holoenzyme with the aim of improving existing models. The individual components, core enzyme (E) and sigma-factor (sigma), were highlighted by deuterium labeling and their center-to-center distances determined in the monomeric and the dimeric holoenzyme. The following distance parameters were obtained: dE1-sigma 1 = 8.6(+/- 1) nm, dE1-E2 = 11.5(+/- 1) nm, d sigma 1-sigma 2 = 12.0(+/- 0.7) nm, dE1-sigma 2 = 9(+/- 3) nm. Using a triangulation procedure the position of the sigma-factors, sigma 1 and sigma 2, were determined with respect to the mass center of the core enzyme molecules, E1 and E2, assuming a symmetrical arrangement of the holoenzyme molecules in the dimer (C2 symmetry). In addition, the orientation of the sigma-factor with respect to core enzyme was estimated by means of model calculations. The obtained model of holoenzyme depicts the sigma-factor as buried in a groove of core enzyme, probably between the large subunits beta' and beta.
J Mol Biol 1991 Jun 20
PMID:Spatial arrangement of sigma-factor and core enzyme of Escherichia coli RNA polymerase. A neutron solution scattering study. 205 37

The assembly of alpha-ketoglutarate dehydrogenase complex (KGDC) has been studied in wild-type Saccharomyces cerevisiae and in respiratory-deficient strains (pet) with mutations in KGD1 and KGD2, the structural genes for alpha-ketoglutarate dehydrogenase (KE1) and dihydrolipoyl transsuccinylase (KE2) components, respectively. Mutants unable to express KE1 or KE2 form partial complexes similar to those reported in earlier studies on the resolution and reconstitution of bacterial and mammalian KGDC. Thus mutants lacking KE1 assemble a high-molecular-weight subcomplex consisting of a KE2 core particle with bound dihydrolipoyl dehydrogenase (E3). Similarly, mitochondrial extracts of mutants lacking KE2 contain dimeric KE1 and E3. These components, however, are not associated with each other. The partial complexes detected in the mutants are capable of reconstituting normal KGDC when supplied with the missing subunit. Complete restoration of overall alpha-ketoglutarate dehydrogenase activity is achieved by mixing appropriate ratios of mitochondrial extracts from mutants deficient in KE1 and KE2. The reconstitution of enzymatic activity correlates with binding of KE1 to the KE2-E3 particle to form a complex with the same sedimentation properties as wild-type KGDC. Overexpression of KE2 relative to KE1 results in a preponderance of incompletely assembled complexes with substoichiometric contents of KE1. Formation of a complex with a full complement of KE1 therefore depends on a balanced output of KE1 and KE2 from their respective genes. Biochemical screens of a pet mutant collection have led to the identification of a new gene required for the expression of enzymatically active KGDC. Mitochondria of the mutant have all of the catalytic subunits of KGDC. Sedimentation analysis of these components indicates that while the mutant has a stable KE2-E3 subcomplex, the interaction of KE1 with KE2 core is much weaker in the mutant than in the wild type. The gene product responsible for this phenotype, therefore, appears to function at a late stage of assembly of KGDC, most likely by posttranslational modification of one of the subunits.
Mol Cell Biol 1991 Aug
PMID:In vivo assembly of yeast mitochondrial alpha-ketoglutarate dehydrogenase complex. 207

We have characterized three cDNA clones corresponding to proteins CM1, CM3 and CM16, which represent the three types of subunits of the wheat tetrameric inhibitor of insect alpha-amylases. The deduced amino acid sequences of the mature polypeptides are homologous to those of the dimeric and monomeric alpha-amylase inhibitors and of the trypsin inhibitors. The mature polypeptides are preceded by typical signal peptides. Southern blot analysis of appropriate aneuploids, using the cloned cDNAs as probes, has revealed the location of genes for subunits of the CM3 and of the CM16 type within a few kb of each other in chromosomes 4A, 4B and 4D, and those for the CM 1 type of subunit in chromosomes 7A, 7B and 7D. Known subunits of the tetrameric inhibitor corresponding to genes from the B and D genomes have been previously characterized. No proteins of this class have been found to be encoded by the A genome in hexaploid wheat (genomes AA, BB, DD) or in diploid wheats (AA) and no anti alpha-amylase activity has been detected in the latter, so that the A-genome genes must be either silent (pseudogenes) or expressed at a much lower level.
Plant Mol Biol 1990 May
PMID:Cloning of cDNA and chromosomal location of genes encoding the three types of subunits of the wheat tetrameric inhibitor of insect alpha-amylase. 210 61

The amino acid sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum has been fitted to the electron density maps. The resulting protein model has been refined to a nominal resolution of 1.7 A using the constrained-restrained least-squares refinement program of Sussman and the restrained least-squares refinement program of Hendrickson & Konnert. The crystallographic refinement, based on 76,452 reflections with F greater than sigma (F) in the resolution range 5.5 to 1.7 A resulted in a crystallographic R-factor of 18.0%. The asymmetric unit contains one dimeric ribulose-1,5-biphosphate carboxylase molecule, consisting of 869 amino acid residues and 736 water molecules. The geometry of the refined model is close to ideal, with root-mean-square deviations of 0.018 A in bond lengths and 2.7 degrees in bond angles. Two loop regions, comprising residues 54 to 63 and 324 to 335, and the last ten amino acid residues at the C terminus are disordered in our crystals. The expected trimodal distribution is obtained for the side-chain chi 1-angles with a marked preference for staggered conformation. The hydrogen-bonding pattern in the N-terminal beta-sheet and the parallel sheet in the beta/alpha-barrel is described. A number of hydrogen bonds and salt bridges are involved in domain-domain and subunit-subunit interactions. The subunit-subunit interface in the dimer covers an area of 2800 A2. Considerable deviations from the local 2-fold symmetry are found at both the N terminus (residues 2 to 5) and the C terminus (residues 422 to 457). Furthermore, loop 8 in the beta/alpha-barrel domain has a different conformation in the two subunits. A number of amino acid side-chains have different conformations in the two subunits. Most of these residues are located at the surface of the protein. An analysis of the individual temperature factors indicates a high mobility of the C-terminal region and for some of the loops at the active site. The positions and B-factors for 736 solvent sites have been refined (average B: 45.9 A2). Most of the solvent molecules are bound as clusters to the protein. The active site of the enzyme, especially the environment of the activator Lys191 in the non-activated enzyme is described. Crystallographic refinement at 1.7 A resolution clearly revealed the presence of a cis-proline at the active site. This residue is part of the highly conserved region Lys166-Pro167-Lys168.
J Mol Biol 1990 Feb 20
PMID:Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution. 210 19

The retroviral genome consists of two identical RNA molecules joined at their 5' ends by the Dimer Linkage Structure (DLS). To study the mechanism of dimerization and the DLS of HIV-1 RNA, large amounts of bona fide HIV-1 RNA and of mutants have been synthesized in vitro. We report that HIV-1 RNA forms dimeric molecules and that viral nucleocapsid (NC) protein NCp15 greatly activates dimerization. Deletion mutagenesis in the RNA 5' 1333 nucleotides indicated that a small domain of 100 nucleotides, located between positions 311 to 415 from the 5' end, is necessary and sufficient to promote HIV-1 RNA dimerization. This dimerization domain encompasses an encapsidation element located between the 5' splice donor site and initiator AUG of gag and shows little sequence variations in different strains of HIV-1. Furthermore, cross-linking analysis of the interactions between NC and HIV-1 RNA (311 to 415) locates a major contact site in the encapsidation element of HIV-1 RNA. The genomic RNA dimer is tightly associated with nucleocapsid protein molecules in avian and murine retroviruses, and this ribonucleoprotein structure is believed to be the template for reverse transcription. Genomic RNA-protein interactions have been analyzed in human immunodeficiency virus (HIV) virions and results showed that NC protein molecules are tightly bound to the genomic RNA dimer. Since retroviral RNA dimerization and packaging appear to be under the control of the same cis element, the encapsidation sequences, and trans-acting factor, the NC protein, they are probably related events in the course of virion assembly.
J Mol Biol 1990 Dec 05
PMID:Cis elements and trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1. 212 74

The water-snake Liophis miliaris presents hemoglobin which binds organic polyphosphate through a simple single-site per tetramer (Mol. Wt. 64500) as judged by titration curves of reduced nicotinamide adenine dinucleotide phosphate either in the presence or absence of inositol hexaphosphate. The site seems to have the same structural nature of that found on other hemoglobins and is able to strongly bind most of the known protein effectors such as inositol hexaphosphate, adenosine triphosphate or 2,3-diphosphoglicerate. The high association constant at pH 7 of reduced nicotinamide for the deoxy hemoglobin of about K(D) = 7 x 10(6) M-1 compared to human hemoglobin (K(D) = 7 x 10(5) M-1), and to that of adenosine triphosphate (its natural erythrocytic polyphosphate) still higher of about K(D) = 10(11) M-1, shows clearly the very high affinity of this snake hemoglobin for such allosteric effector. The results besides corroborating the dimer-tetramer transition mechanism proposed to describe the oxygen transport by the hemoglobin of Liophis miliaris--may explain the difficulties to obtain the oxy dimeric conformation of the protein by usual hemolysis and stripped off procedures.
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PMID:Polyphosphate binding sites in Liophis miliaris hemoglobin. Evidence with reduced nicotinamide adenine dinucleotide phosphate. 213 36

Escherichia coli integration host factor (IHF) is a small dimeric protein that binds to a specific DNA consensus sequence and produces DNA bending. Transcription from the bacteriophage lambda pL promoter is stimulated three- to fourfold by IHF both in vivo and in vitro. IHF binds with high-affinity to two tandem sites located just upstream from the pL promoter and enhances the formation of RNA polymerase-promoter closed complexes. The rate of isomerization to open complex is not influenced by IHF. IHF may stimulate recognition of pL by one or more of several mechanisms: (1) by bending DNA; (2) by making protein-protein contacts with RNA polymerase; or (3) by occluding a competing promoter upstream from pL.
J Mol Biol 1990 May 05
PMID:Integration host factor stimulates the phage lambda pL promoter. 214 Jan 36

A novel molecule from the arylalkylamine family of drugs, KHL-8430, has been identified as a potent and specific inhibitor of calmodulin activity. The effect of this drug on calmodulin-mediated enzymatic actions has been analyzed to exemplify how to model the mechanism of action of a functional calmodulin antagonist. The approach used includes both binding and enzyme kinetic studies. In both types of experiments, the effects of drugs on calmodulin-phosphofructokinase [ATP:D[fructose-6-phosphate-1-phosphotransferase, EC 2.7.1.11] and calmodulin-phosphodiesterase (3':5' cyclic nucleotide phosphodiesterase, EC 3.6.1.3) interactions have been investigated. We have found that KHL-8430, in contrast to trifluoperazine, a classical anticalmodulin drug, competes with neither phosphofructokinase nor phosphodiesterase for calmodulin binding, yet it liberates phosphofructokinase from calmodulin inhibition and phosphodiesterase from calmodulin stimulation. The anticalmodulin activity occurs at lower KHL-8430 than trifluoperazine concentrations. These findings might establish the functional importance of these differences in the specificity of these drugs. The synthesis of the data suggests that (i) whereas trifluoperazine antagonizes both phosphofructokinase and phosphodiesterase binding to calmodulin, KHL-8430 interacts with calmodulin complexed with enzymes; (ii) KHL-8430 binds to the calmodulin-phosphofructokinase complex with an affinity constant of 0.8 microM, whereas the binding constant of trifluoperazine is 2.5 microM (iii) within the ternary complex the dimeric form of the kinase preserves activity that is otherwise inactive; and (iv) the binding of trifluoperazine and KHL-8430 to calmodulin exhibits negative cooperativity. The approach used in this study makes it possible to screen for the calmodulin antagonist effect of other drugs as well.
Mol Pharmacol 1990 Dec
PMID:Dissimilar mechanisms of action of anticalmodulin drugs: quantitative analysis. 214 57

Europium luminescence from europium bound to sarcoplasmic reticulum (Ca2+ + Mg2+)-ATPase indicates that there are two high affinity calcium binding sites. Furthermore, the two calcium ions at the binding sites are highly coordinated by the protein as the number of H2O molecules surrounding the Ca2+ ions are 3 and 0.5. In the presence of ATP, calcium ions are occluded even further down to 2 and zero H2O molecules, respectively. The Ca2+ - Ca2+ intersite distance is estimated to be 8-9 A and the average distance from the Ca2+ sites to CrATP is about 18 A. Digestion of the (Ca2+ + Mg2+)-ATPase at the T2 site (Arg 198) causes uncoupling of Ca2(+)-transport from ATPase activity while calcium occlusion due to E1-P formation remains unchanged. Further tryptic digestion beyond T2 and in the presence of ATP diminishes Ca2+ occlusion to zero while 50% of the ATPase hydrolytic activity remains. Tryptic digestion beyond T2 and in the absence of ATP diminishes ATPase hydrolytic activity to 50% of normal while Ca2+ occlusion remains intact. These data are consistent with a mechanism in which the functional enzyme must be in the dimeric form for occlusion and calcium uptake to occur, but each monomer can hydrolyze ATP.
Mol Cell Biochem 1990 Dec 20
PMID:Tertiary structure and energy coupling in Ca2(+)-pump system. 214 85

A new variant of human glucose 6-phosphate dehydrogenase (G6PD), provisionally designated G6PD Harilaou, was observed in a Greek boy affected by severe hemolytic anemia. G6PD Harilaou was associated with very severe deficiency of enzyme activity, which measured about 1% of normal in the patient's fibroblasts. By fusion of Harilaou fibroblasts with a similarly enzyme-deficient mutant CHO cell line, we have isolated a hybrid cell line that has a G6PD activity 5-10 times higher than either of the parental cells. By electrophoretic analysis we show that most of this activity is associated with a hybrid dimeric G6PD molecule consisting of one hamster and one human subunit. We suggest that this heterologous quasi-interallelic complementation is effected by a catalytically abnormal hamster subunit stabilizing a catalytically abnormal and unstable Harilaou subunit. This approach may be useful for the study of dimer formation and stability in human G6PD.
Somat Cell Mol Genet 1990 Mar
PMID:Intragenic interspecific complementation of glucose 6-phosphate dehydrogenase in human-hamster cell hybrids. 215 98


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