Abstract:
:R67 dihydrofolate reductase (DHFR) is a type II DHFR produced by bacteria as a resistance mechanism to the increased clinical use of the antibacterial drug trimethoprim. Type II DHFRs are not homologous in either sequence or structure with chromosomal DHFRs. The type II enzymes contain four identical subunits which form a homotetramer containing a single active site pore accessible from either end. Although the crystal structure of the complex of R67 DHFR with folate has been reported [Narayana et al. (1995) Nat. Struct. Biol. 2, 1018], the nature of the ternary complex which must form with substrate and cofactor is unclear. We have performed transferred NOE and interligand NOE (ILOE) studies to analyze the ternary complexes formed from NADP(+) and folate in order to probe the structure of the ternary complex. Consistent with previous studies of the binary complex formed from another type II DHFR, the ribonicotinamide bond of NADP(+) was found to adopt a syn conformation, while the adenosine moiety adopts an anti conformation. Large ILOE peaks connecting NADP(+) H4 and H5 with folate H9 protons are observed, while the absence of a large ILOE connecting NADP(+) H4 and H5 with folate H7 indicates that the relative orientation of the two ligands differs significantly from the orientation in the chromosomal enzyme. To obtain more detailed insight, we prepared and studied the folate analogue 2-deamino-2-methyl-5,8-dideazafolate (DMDDF) which contains additional protons in order to provide additional NOEs. For this analogue, the exchange characteristics of the corresponding ternary complex were considerably poorer, and it was necessary to utilize higher enzyme concentrations and higher temperature in order to obtain ILOE information. The results support a structure in which the NADP(+) and folate/DMDDF molecules extend in opposite directions parallel to the long axis of the pore, with the nicotinamide and pterin ring systems approximately stacked at the center. Such a structure leads to a ternary complex which is in many respects similar to the gas-phase theoretical calculations of the dihydrofolate-NADPH transition state by Andres et al. [(1996) Bioorg. Chem. 24, 10-18]. Analogous NMR studies performed on folate, DMDDF, and R67 DHFR indicate formation of a ternary complex in which two symmetry-related binding sites are occupied by folate and DMDDF.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Li D,Levy LA,Gabel SA,Lebetkin MS,DeRose EF,Wall MJ,Howell EE,London REdoi
10.1021/bi0026425subject
Has Abstractpub_date
2001-04-10 00:00:00pages
4242-52issue
14eissn
0006-2960issn
1520-4995pii
bi0026425journal_volume
40pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::In the ATP-dependent carboxylation of biotin that is catalyzed by most biotin-dependent carboxylases, a fundamental mechanistic question is whether the ATP activates bicarbonate (via the formation of carboxyphosphate as an intermediate) or whether the ATP activates biotin (via the formation of O-phosphobiotin). We hav...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00421a009
更新日期:1988-10-18 00:00:00
abstract::Oligodeoxynucleotides modified site-specifically with dG-(+)-trans- and dG-(+)-cis-anti-BPDE (7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene) or dG-(-)-trans- and dG-(-)-cis-anti-BPDE were used as templates in primer extension reactions catalyzed by the Klenow fragment of Escherichia coli DNA polymerase I....
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00080a027
更新日期:1993-07-27 00:00:00
abstract::A new class of bacterial multisubunit membrane-bound electron-transfer complexes has been identified based on biochemical and bioinformatic data. It contains subunits homologous to the three-subunit molybdopterin oxidoreductases and four additional subunits, two of which are c-type cytochromes. The complex was purifie...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi047267l
更新日期:2005-08-02 00:00:00
abstract::Near-infrared FT-Raman spectroscopy can be used to measure the vibrations of the bacteriorhodopsin (bR) chromophore without the disadvantage of conventional visible resonance Raman spectroscopy, where the visible excitation drives the bR photoreactions. We utilized this technique to investigate the light-dark adaptati...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00060a020
更新日期:1993-03-09 00:00:00
abstract::Fourier transform infrared spectra of light-adapted bacteriorhodopsin exhibit a band at 1618 cm(-1) that shifts to 1625 cm(-1) upon formation of the L intermediate. It is assigned to the peptide C==O of Val49 from the fact that it shifts in [1-(13)C]valine-labeled bacteriorhodopsin and appears perturbed in the Val49--...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9524530
更新日期:1996-04-02 00:00:00
abstract::Tyrosine phenol-lyase, a tetrameric pyridoxal 5'-phosphate dependent enzyme, catalyzes the reversible hydrolytic cleavage of L-tyrosine to phenol and ammonium pyruvate. Here we describe the crystal structure of the Citrobacter freundii holoenzyme at 1.9 A resolution. The structure reveals a network of protein interact...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0601858
更新日期:2006-06-20 00:00:00
abstract::The thermodynamic binding parameters and crystal structure for streptavidin-peptide complexes where the peptide sequences were obtained by random screening methods are reported. The affinities between streptavidin and two heptapeptides were determined by titrating calorimetric methods [Phe-Ser-His-Pro-Gln-Asn-Thr, Ka ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00154a004
更新日期:1992-10-06 00:00:00
abstract::Helicases are enzymes that use energy from nucleoside triphosphate hydrolysis to unwind double-stranded (ds) DNA, a process vital to virtually every phase of DNA metabolism. Helicases have been classified as either 5'-to-3' or 3'-to-5' on the basis of their ability to unwind duplex DNA adjacent to either a 5' or 3' si...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi012058b
更新日期:2002-02-19 00:00:00
abstract::Thermal pertubation difference spectra of sperm whale myoglobin (Mb) and soybean leghemoglobin a (Lb a) in the near-ultraviolet reveal similarities in the tryptophan environment of the two proteins. Of the two tryptophans in each protein, one has its indolyl NH group fully exposed to aqueous solvent, while the other b...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00620a009
更新日期:1977-01-11 00:00:00
abstract::The function of the GM2 activator protein is to act as a substrate-specific cofactor in the hydrolysis of GM2 ganglioside by beta-hexosaminidase A. Mutations in the gene encoding it result in the AB variant form of GM2 gangliosidosis. One such mutation, Cys138 Arg, results in the mutant protein being retained and degr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi971211s
更新日期:1998-01-20 00:00:00
abstract::Electrostatic interactions play a key role in enzyme catalytic function. At long range, electrostatics steer the incoming ligand/substrate to the active site, and at short distances, electrostatics provide the specific local interactions for catalysis. In cases in which electrostatics determine enzyme function, orthol...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi026918f
更新日期:2003-04-01 00:00:00
abstract::The thermodynamic parameters characterizing the interaction between rabbit fast skeletal muscle troponin and tropomyosin have been determined at 25 degrees C for three solution conditions: buffer containing (A) 1 mM CaCl2, simulating a "turned-on" state, (B) 3 mM MgCl2, simulating a "turned-off" state, and (C) 2 mM et...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00340a040
更新日期:1985-09-10 00:00:00
abstract::Recent studies implicate hydrogen sulfide (H2S) oxidation as an important aspect of bacterial antibiotic resistance and sulfide homeostasis. The cst operon of the major human pathogen Staphylococcus aureus is induced by exogenous H2S stress and encodes enzymes involved in sulfide oxidation, including a group I flavopr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00714
更新日期:2016-11-29 00:00:00
abstract::The interaction of the zinc finger protein WT1 with RNA aptamers has been investigated using a quantitative binding assay, and the results have been compared to those from a previous study of the DNA binding properties of this protein. A recombinant peptide containing the four zinc fingers of WT1 (WT1-ZFP) binds to re...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi001941r
更新日期:2001-02-20 00:00:00
abstract::A study of the dynamics and mechanism of the various thermotropic phase transitions undergone by the hydrated monoacylglycerides monoolein and monoelaidin, in the temperature range of 20-120 degrees C and from 0 to 5 M NaCl, has been undertaken. Measurements were made by using time-resolved X-ray diffraction at the Co...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00394a008
更新日期:1987-10-06 00:00:00
abstract::Temporins are short (10-13 amino acids) and linear antimicrobial peptides first isolated from the skin of the European red frog, Rana temporaria, and are effective against Gram-positive bacteria and Candida albicans. To get insight into their mechanism(s) of action, we compared the effects on model membranes exerted b...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi011929e
更新日期:2002-04-02 00:00:00
abstract::Engineering proteins to withstand a broad range of conditions continues to be a coveted objective, holding the potential to advance biomedicine, industry, and our understanding of disease. One way of achieving this goal lies in elucidating the underlying interactions that define protein stability. It has been shown th...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0600143
更新日期:2006-03-07 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::We have synthesized a series of N-propylamino-substituted benzazepinones (NPSBs) as specific probes for the benzothiazepinone (BTZ) binding domain of muscle L-type calcium channels (LTCCs). NPSBs were identified which possess high affinity for the channel after purification. We synthesized a fluorescent NPSB, DMBODIPY...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00010a039
更新日期:1995-03-14 00:00:00
abstract::Heme-derived linear tetrapyrroles (phytobilins) in phycobiliproteins and phytochromes perform critical light-harvesting and light-sensing roles in oxygenic photosynthetic organisms. A key enzyme in their biogenesis, phycocyanobilin:ferredoxin oxidoreductase (PcyA), catalyzes the overall four-electron reduction of bili...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi100728q
更新日期:2010-07-27 00:00:00
abstract::Multidrug resistance protein (MRP) and P-glycoprotein (Pgp) are both members of the superfamily of ATP binding cassette plasma membrane drug transport proteins, which may be partly responsible for multidrug resistance of tumor cells. Although MRP has been identified as an organic anion transporter and Pgp as a transpo...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9718043
更新日期:1998-02-24 00:00:00
abstract::The high resolution proton nuclear magnetic resonance (NMR) spectra of the synthetic DNA block polymer d(C15A15)-d(T15G15) were studied in order to more completely understand telestability in DNA, and to provide fundamental NMR data on DNA helices and random coils. Spectra were measured in the spectral region from 0 t...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00622a031
更新日期:1977-02-08 00:00:00
abstract::[1-Penicillamine,2-leucine]oxytocin is a conformationally restricted analogue of oxytoxin in which the half-cystine-1 and tyrosine-2 residues of the native hormone are replaced by half-penicillamine (beta, beta-dimethyl-half-cystine) and leucine, respectively. This analogue is a surprisingly potent oxytocin antagonist...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00513a018
更新日期:1981-05-12 00:00:00
abstract::Brd4 belongs to the BET family. It is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. With its tandem bromodomains, Brd4 avidly binds to diacetylated H4-AcK5/K1...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi8001659
更新日期:2008-06-17 00:00:00
abstract::Interaction of a mitochondria-specific anionic phospholipid, cardiolipin (CL), with an intermembrane protein, cytochrome c (cyt c), yields a peroxidase complex. During apoptosis, the complex induces accumulation of CL oxidation products that are essential for detachment of cyt c from the mitochondrial membrane, induct...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi801507s
更新日期:2008-12-23 00:00:00
abstract::The technique of fluorescence recovery after photobleaching is used to perform an extensive study of the lateral diffusion of a phospholipid probe in the binary mixture dimyristoylphosphatidylcholine/cholesterol, above the melting temperature of the phospholipid. In the regions of the phase diagram where a single liqu...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00144a013
更新日期:1992-07-28 00:00:00
abstract::The far-ultraviolet circular dichroism spectra of bovine and human prothrombin, prothrombin fragment 1, prethrombin 1, prothrombin fragment 2, and prethrombin 2 (prethrombin 2des(1--13)) were determined and the method of Chen et al. [Chen, Y. H., Yang, J. T., & Martinez, H. M. (1972) Biochemistry 11, 4120--4131; Chen,...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00577a017
更新日期:1979-05-15 00:00:00
abstract::Electron paramagnetic resonance (EPR) at 15 K was used to probe the magnetic interaction between the visible copper CuA2+ and ferric cytochrome a in the carbon monoxide compound of beef heart cytochrome oxidase. At pH 8.6, the midpoint potentials (Em's) for one-electron oxidation of CuA+ and cytochrome a2+ were found ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00330a028
更新日期:1985-04-23 00:00:00
abstract::Phthalate dioxygenase from Pseudomonas cepacia contains a mononuclear ferrous center that is strictly required for catalytic oxygen activation. The spectroscopic characterization of this iron site and its ligand interactions has been complicated in the past by interference from a Rieske-type binuclear (2Fe-2S) cluster...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00069a017
更新日期:1993-05-11 00:00:00
abstract::Hypochlorous acid (HOCl) is a powerful oxidant generated from H(2)O(2) and Cl(-) by the heme enzyme myeloperoxidase, which is released from activated leukocytes. HOCl possesses potent antibacterial properties, but excessive production can lead to host tissue damage that is implicated in a wide range of human diseases ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi060348s
更新日期:2006-07-04 00:00:00