Abstract：
:The NikR transcription factor from Escherichia coli is a Ni(II)-dependent repressor that regulates production of the nickel ion transporter encoded by the nik operon. In the previous paper in this issue (Wang, S. C., Dias, A., Bloom, S. L., and Zamble, D. B. (2004) Selectivity of Metal Binding and Metal-Induced Stability of Escherichia coli NikR, Biochemistry 43, 10018-10028) we demonstrated that NikR can bind 1 equiv of Ni(II) or several other divalent transition metals with similar affinities, but that the Ni(II)-loaded protein is less susceptible to thermal or chemical denaturation than other divalent metal complexes. Here, we investigate the metal selectivity of the DNA-binding activity of NikR. Stoichiometric nickel induces binding of nanomolar NikR to the recognition sequence in the nik promoter, but single equivalents of other divalent metals such as Cd(II), Co(II), and Cu(II) also induce a similar DNA-binding affinity. In the presence of excess nickel, DNA-binding experiments indicate that NikR binds to the nik promoter as a tetramer with much higher affinity (20 pM), and it is this response that is selective for nickel. The DNA binding induced by an excess of other divalent metals is weaker, and is enhanced by the addition of stoichiometric nickel. Nickel titrations into a DNA-binding assay reveal a nickel affinity of 30 nM for a second metal-binding site, and in the presence of 30 nM metal only nickel induces detectable DNA binding by Ni(II)-NikR. These experiments support the hypothesis that there are two metal-binding sites and that both contribute to the nickel-selective DNA-binding response. A model for the in vivo activity of NikR is discussed.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Bloom SL,Zamble DBdoi
10.1021/bi049404ksubject
Has Abstractpub_date
2004-08-10 00:00:00pages
10029-38issue
31eissn
0006-2960issn
1520-4995journal_volume
43pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:A strategy to design potent antagonists of human coagulation factor VIIa (FVIIa) by linking two proteins that independently inhibit activity and bind at separate, nonoverlapping sites is presented. A bifunctional inhibitor (KDTF5), comprising a Kunitz-type domain engineered to inhibit the FVIIa active site and a solub...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi970388j
更新日期：1997-05-13 00:00:00
abstract：:The stability of three forms of glucoamylase from Aspergillus niger has been investigated by differential scanning and isothermal titration calorimetry: Glucoamylase 1 (GA1), which consists of a catalytic domain and a starch-binding domain (SBD) connected by a heavily O-glycosylated linker region; glucoamylase 2 (GA2)...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi990185q
更新日期：1999-05-11 00:00:00
abstract：:Myosin cross-bridge subfragment 1 (S1) is the ATP catalyzing motor protein in muscle. It consists of three domains that catalyze ATP and bind actin (catalytic), conduct energy transduction (converter), and transport the load (lever arm). Force development during contraction is thought to result from rotary lever arm m...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi002387o
更新日期：2001-04-17 00:00:00
abstract：:We have investigated the role of the labile terminal domains of the core histones on the stability of the subunits of the protein core of the nucleosome by studying the thermodynamic behavior of the products of limited trypsin digestion of these subunits. The thermal stabilities of the truncated H2A-H2B dimer and the ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0110140
更新日期：2001-10-30 00:00:00
abstract：:Clustering of anionic lipids away from zwitterionic ones by cationic antimicrobial agents has recently been established as a mechanism of action of natural small, flexible peptides as well as non-natural synthetic peptide mimics. One of the largest classes of antimicrobial peptides consists of peptides that form catio...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi100378m
更新日期：2010-05-18 00:00:00
abstract：:HIV-1 Vif is an accessory protein that induces the proteasomal degradation of the host restriction factor, apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G). The N-terminal half of Vif binds to APOBEC3G, and the C-terminal half binds to subunits of a cullin 5-based ubiquitin ligase. This Vi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi201738a
更新日期：2012-03-13 00:00:00
abstract：:The multicatalytic proteinase complex (MPC, proteasome) is composed of 28 subunits organized into four rings surrounding a water-filled canal. The catalytic centers face the inner canal confining protein substrates to an enclosed space. Experimental findings obtained with MPC from archaebacteria suggest that degradati...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi990826h
更新日期：1999-11-02 00:00:00
abstract：:Secretory carrier membrane protein 2 (SCAMP2) functions in late steps of membrane fusion in calcium-dependent granule exocytosis. A basic/hydrophobic peptide segment within SCAMP2 (SCAMP2 E: CWYRPIYKAFR) has been implicated in this function and shown to bind and sequester phosphatidylinositol 4,5-bisphosphate [PI(4,5)...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi701121j
更新日期：2007-09-25 00:00:00
abstract：:Kynureninase is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the hydrolytic cleavage of l-kynurenine to give l-alanine and anthranilic acid. beta-Benzoyl-l-alanine, the analogue of l-kynurenine lacking the aromatic amino group, was shown to a good substrate for kynureninase from Pseudomonas fluorescens, an...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi100955b
更新日期：2010-09-14 00:00:00
abstract：:Glycosylases specifically recognize and flip their target base out of the DNA helix into the enzyme's active site. Our simulations show that a partially flipped state, already present in free DNA carrying a T:G mispair, becomes the more probable state compared to the closed state after binding of thymine DNA glycosyla...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.8b00409
更新日期：2018-10-02 00:00:00
abstract：:The ligand-binding dynamics and the reaction with O(2) of the fully (five-electron) reduced cytochrome caa(3) from the thermohalophilic bacterium Rhodothermus (R.) marinus were investigated. The enzyme is a proton pump which has all the residues of the proton-transfer pathways found in the mitochondrial-like enzymes c...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi010344h
更新日期：2001-09-04 00:00:00
abstract：:The N-terminal 17% of apolipoprotein B (apoB-17) is secreted lipid-poor while apoB-41 particles are secreted with a triacylglycerol (TAG)-rich core. Thus, the sequence between apoB-17 and apoB-41 is necessary for the assembly of TAG-rich lipoproteins. To delineate this region, C127 cells were permanently transfected t...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi000791h
更新日期：2000-08-15 00:00:00
abstract：:Acetohydroxy acid synthase (AHAS) is a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the first common step in the biosynthesis of branched-chain amino acids, condensation of pyruvate with a second 2-ketoacid to form either acetolactate or acetohydroxybutyrate. AHAS isozyme II from Escherichia coli is spec...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi102051h
更新日期：2011-04-19 00:00:00
abstract：:In refolding of iso-2 cytochrome c from Saccharomyces cerevisiae, there are two slow folding reactions, tau 1a and tau 1b. The slower of the slow reactions, tau 1a = 100-200 s, is observed only by absorbance changes, while tau 1b (10-20-fold faster) is detected by fluorescence changes. The temperature dependence of th...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00348a024
更新日期：1985-12-31 00:00:00
abstract：:Superoxide reductase (SOR) is an Fe protein that catalyzes the reduction of superoxide to give H(2)O(2). Recently, the mutation of the Glu47 residue into alanine (E47A) in the active site of SOR from Desulfoarculus baarsii has allowed the stabilization of an iron-peroxo species when quickly reacted with H(2)O(2) [Math...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0498151
更新日期：2004-07-13 00:00:00
abstract：:The complete amino acid sequence of the major component myoglobin from the dwarf sperm whale, Kogia simus, was determined by specific cleavage of the protein to obtain large peptides which are readily degraded by the automatic sequenator. Three easily separable peptides were obtained by cleaving the protein at its two...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00624a010
更新日期：1977-03-08 00:00:00
abstract：:Polyadenylated RNA was isolated from nuclei of cultured Drosophila cells, Schneider's line 2, and used as a template to synthesize a complementary DNA probe. Hybridization experiments were performed to study the relationship between nuclear and cytoplasmic RNA. About two-thirds of the nuclear polyadenylated RNA sequen...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00656a026
更新日期：1976-06-01 00:00:00
abstract：:S100 proteins are small dimeric members of the EF-hand superfamily of Ca(2+) binding proteins thought to participate in mediating intracellular Ca(2+) signals by binding to and thereby regulating target proteins in a Ca(2+)-dependent manner. As dimer formation is crucial to S100 function, we applied a yeast two-hybrid...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi000257+
更新日期：2000-08-08 00:00:00
abstract：:Using cysteine mutagenesis and chemical modification by methanethiosulfonate derivatives, it was demonstrated that the external putative loop, joining transmembrane segments (TM's) IV-V of rabbit Na+/glucose cotransporter, rSGLT1, forms part of a Na+ binding and voltage sensing domain. Within this region, exposure to ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi052267m
更新日期：2006-04-11 00:00:00
abstract：:Nephrocalcin (NC), a calcium-binding glycoprotein of 14,000 molecular weight as a monomer, is known to inhibit the growth of calcium oxalate monohydrate (COM) crystals in renal tubules. We have isolated NC from bovine kidney tissue and purified into four isoforms, fractions A-D. NC-A and NC-B strongly inhibit the grow...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi961200j
更新日期：1996-11-26 00:00:00
abstract：:The interaction of alamethicin with artificial lecithin multilamellar dispersions was investigated by nuclear magnetic resonance (NMR) and Raman spectroscopies. 31P NMR studies revealed perturbation of the lipid head groups in the presence of the icosapeptide. Simulation of the 31P NMR spectra indicated that the obser...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00347a019
更新日期：1985-12-17 00:00:00
abstract：:A minor fraction of plasma high-density lipoprotein (pre beta-1 HDL) has been shown to promote cholesterol efflux from peripheral cell membranes [Castro, G. R., & Fielding, C. J. (1988) Biochemistry 27, 25-29]. When isolated native plasma is incubated at 37 degrees C, this fraction is specifically decreased. On the ot...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00160a022
更新日期：1992-11-17 00:00:00
abstract：:Hybridization to RNA is important for many applications, including antisense therapeutics, RNA interference, and microarray screening. Similar thermodynamic stabilities of A-U and G-U base pairs result in difficulties in selective binding to RNA. Moreover, A-U pairs are weaker than G-C pairs so that binding is sometim...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi901506f
更新日期：2009-11-24 00:00:00
abstract：:The cAMP-dependent protein kinase (cAPK) plays an essential role during differentiation and fruit morphogenesis in Dictyostelium discoideum. The presence of an open reading frame on the gene, pkaC (previously named either Dd PK2 or Dd PK3 by different groups), predicts a 73-kDa polypeptide with 54% similarity to the c...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00088a003
更新日期：1993-09-21 00:00:00
abstract：:Tropomyosin is postulated to confer stability to actin filaments in nonmuscle cells. We have found that a nonmuscle tropomyosin isolated from the intestinal epithelium can directly stabilize actin filaments by slowing depolymerization from the pointed, or slow-growing, filament end. Kinetics of elongation and depolyme...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00447a035
更新日期：1989-10-17 00:00:00
abstract：:Heparin was carboxyl-reduced with sodium boro[3H]hydride and converted to a mixture of oligosaccharides by treatment with nitrous acid at pH 2. The oligosaccharide mixture was aldehyde-reduced with sodium boro[3H]hydride and the mixture of products, labeled both in the hexoses formed in the carboxyl-reduction step and...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00663a006
更新日期：1976-09-07 00:00:00
abstract：:A panel of 10 hybridomas was assembled to assess the influence of various genetic and biological factors upon glycosylation of secreted monoclonal IgG. After exhaustive Pronase digestion of IgG, glycopeptides were characterized chromatographically by apparent size, charge, and concanavalin A (Con A)-Sepharose and Lens...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00429a065
更新日期：1989-02-07 00:00:00
abstract：:Large primary deuterium kinetic isotope effects (1° DKIEs) on enzyme-catalyzed hydride transfer may be observed when the transferred hydride tunnels through the energy barrier. The following 1° DKIEs on kcat/ Km and relative reaction driving force are reported for wild-type and mutant glycerol-3-phosphate dehydrogenas...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.8b00536
更新日期：2018-07-24 00:00:00
abstract：:The light oxygen voltage-sensing (LOV) domain plays a crucial role in blue light (BL) sensing in plants and microorganisms. LOV domains are usually associated with the effector domains and regulate the activities of effector domains in a BL-dependent manner. Photozipper (PZ) is monomeric in the dark state. BL induces ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.7b01045
更新日期：2018-02-06 00:00:00
abstract：:Earlier work indicates that the major DNA repair phosphodiesterase (PDE) in yeast cells is the well-characterized Apn1 protein. Apn1 demonstrates both Mg2+-independent PDE activity and Mg2+-independent class II apurinic/apyrimidinic (AP) endonuclease activity and represents greater than 90% of the activity detected in...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi970048y
更新日期：1997-05-20 00:00:00
