Abstract：
:The bacterial DNA cytosine methyltransferase M.HhaI sequence-specifically modifies DNA in an S-adenosylmethionine dependent reaction. The enzyme stabilizes the target cytosine (GCGC) into an extrahelical position, with a concomitant large movement of an active site loop involving residues 80-99. We used multidimensional, transverse relaxation-optimized NMR experiments to assign nearly 80% of all residues in the cofactor-bound enzyme form, providing a basis for detailed structural and dynamical characterization. We examined details of the previously unknown effects of the cofactor binding with M.HhaI in solution. Addition of the cofactor results in numerous structural changes throughout the protein, including those decorating the cofactor binding site, and distal residues more than 30 A away. The active site loop is involved in motions both on a picosecond to nanosecond time scale and on a microsecond to millisecond time scale and is not significantly affected by cofactor binding except for a few N-terminal residues. The cofactor also affects residues near the DNA binding cleft, suggesting a role for the cofactor in regulating DNA interactions. The allosteric properties we observed appear to be closely related to the significant amount of dynamics and dynamical changes in response to ligand binding detected in the protein.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Zhou H,Shatz W,Purdy MM,Fera N,Dahlquist FW,Reich NOdoi
10.1021/bi602662esubject
Has Abstractpub_date
2007-06-19 00:00:00pages
7261-8issue
24eissn
0006-2960issn
1520-4995journal_volume
46pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:Phosphorescent probes are described that are quenchable by dioxygen and that partition into membranes. These probes are derivatives of porphyrin, in which the central metal, either zinc or palladium, induces intersystem crossing to enhance the triplet yield. The location of the probe in a suspension of membranes depen...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00474a018
更新日期：1990-06-05 00:00:00
abstract：:Site-directed mutagenesis of the aspartate receptor of Salmonella typhimurium (Tars) at serine 68, a residue located within the aspartate binding pocket and at the subunit interface, identified this residue as an allosteric switch in this receptor. Substitutions at this position can affect both the type and degree of ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi961481v
更新日期：1996-11-26 00:00:00
abstract：:We have studied the structure of the CuB site in the binuclear heme-copper center of the fully oxidized form of the quinol-oxidizing cytochrome aa3-600 from Bacillus subtilis by EXAFS and ENDOR spectroscopy. This enzyme is member of the large superfamily of heme-copper respiratory oxidases, which catalyze the reductio...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00032a019
更新日期：1995-08-15 00:00:00
abstract：:The interaction of pig plasma gelsolin (G) and actin (A) was examined by using photoreactive 4-maleimidobenzophenone-actin (BPM-actin) in which BPM was previously conjugated to Cys-374 of actin through the maleimide moiety. In the presence of micromolar [Ca2+], the major cross-linked product observed after irradiation...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00237a020
更新日期：1991-06-11 00:00:00
abstract：:Adduct-induced DNA damage can affect transcription efficiency and DNA replication and repair. We previously investigated the effects of the 3'-next flanking base (G*CT vs G*CA; G*, FABP, N-(2'-deoxyguanosin-8-yl)-4'-fluoro-4-aminobiphenyl; FAF, N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene) on the conformation of...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi5003212
更新日期：2014-06-24 00:00:00
abstract：:The packing of lipids into different aggregates, such as spheres, rods, or bilayers, is dependent on the hydrophobic volume, the hydrocarbon-water interfacial area, and the hydrocarbon chain length of the participating molecules, according to the self-assembly theory [Israelachvili, J. N., Marcelja, S., & Horn, R. G. ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00371a038
更新日期：1986-11-18 00:00:00
abstract：:In prokaryotes, a large share of the proteins are secreted from the cell through a process that requires their translocation across the cytoplasmic membrane. This process is mediated by the universally conserved Sec system with homologues in the endoplasmic reticulum and thylakoid membranes of eukaryotes. The Sec syst...
journal_title：Biochemistry
pub_type： 杂志文章,评审
doi：10.1021/bi400913x
更新日期：2013-10-01 00:00:00
abstract：:The innate immune response to infection or injury involves an antigen-antibody triggered classical pathway (CP) of complement activation, in which soluble and cell surface plasma proteins cooperatively effect elimination of foreign organisms and damaged host cells. However, protracted or dysfunctional complement activ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi900679r
更新日期：2009-09-08 00:00:00
abstract：:Neutrophil elastase (NE), a mediator of inflammation, binds with high affinity numerous anionic molecules including suramin, a polysulfated naphthylurea, which inhibits it with a Ki of 0.2 microM and a 4:1 suramin:NE stoichiometry and thus constitutes a potential therapeutic agent. In an attempt to locate the suramin ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi971029r
更新日期：1997-12-16 00:00:00
abstract：:Bypass synthesis by DNA polymerase I was studied using synthetic 40-nucleotide-long gapped duplex DNAs each containing a site-specific abasic site analog, as a model system for mutagenesis associated with DNA lesions. Bypass synthesis proceeded in two general stages: a fast polymerization stage that terminated opposit...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9621324
更新日期：1997-02-18 00:00:00
abstract：:Parkinson's disease (PD) involves loss of dopaminergic neurons in the substantia nigra and is characterized by intracellular inclusions, Lewy bodies, consisting primarily of aggregated alpha-synuclein. Two substitution mutations (A53T and A30P) in alpha-synuclein gene have been identified in familial early-onset PD. T...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi036114f
更新日期：2004-05-11 00:00:00
abstract：:Following platelet activation, platelets undergo a dramatic shape change mediated by the actin cytoskeleton and accompanied by secretion of granule contents. While the actin cytoskeleton is thought to influence platelet granule secretion, the mechanism for this putative regulation is not known. We found that disruptio...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi100541t
更新日期：2010-06-01 00:00:00
abstract：:The hairpin catalytic motif in tobacco ringspot virus satellite RNA consists of two helix-loop-helix elements on two adjacent arms of a four-way helical junction. The bases essential for catalytic activity are located in the loops that are brought into proximity by a conformational change as a prerequisite for catalys...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi010773f
更新日期：2001-09-18 00:00:00
abstract：:In efforts to understand the mechanisms of many nucleic acid enzymes, the first site-directed mutations are made at conserved acidic active residues. Almost without exception, the low or null activities of the resulting variants are attributed to the importance of the acidic residue(s) to the ligation of required meta...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi000337d
更新日期：2000-09-05 00:00:00
abstract：:Guanidine hydrochloride (GdnHCl) and thermally induced unfolding measurements on the oxidized form of Escherichia coli thioredoxin at pH 7 were combined for the purpose of assessing the functional dependence of unfolding free energy changes on denaturant concentration over an extended GdnHCl concentration range. Conve...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00135a022
更新日期：1992-05-26 00:00:00
abstract：:Members of the ATP-binding cassette (ABC) transporters share the same basic architecture, with a four-core domain made of two transmembrane plus two nucleotide-binding domains. However, a supramolecular organization has been detected in some ABC transporters, which might be relevant to physiological regulation of subs...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0482809
更新日期：2005-03-22 00:00:00
abstract：:The binding of UDP-N-acetylglucosamine (UDPNAG) to the enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) was studied in the absence and presence of the antibiotic fosfomycin by isothermal titration calorimetry. Fosfomycin binds covalently to MurA in the presence of UDPNAG and also in its absence as demonst...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0107041
更新日期：2001-08-21 00:00:00
abstract：:Two paramagnetic probes, viz., Mn2+ and Cr3+-ATP, were used to map distances to various loci on carbamoyl-phosphate synthetase by using NMR measurements. The paramagnetic influence of Mn2+ on the 1H of L-glutamate and L-ornithine was measured at 200 and 360 MHz. On the basis of these data, a correlation time for the p...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00277a020
更新日期：1983-04-12 00:00:00
abstract：:Probing and interrogating protein interactions that involve acyl carrier proteins (ACP's) in fatty acid synthases and polyketide synthases are critical to understanding the molecular basis for the programmed assembly of complex natural products. Here, we have used unnatural amino acid mutagenesis to site specifically ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi500936u
更新日期：2014-12-09 00:00:00
abstract：:Two oxygenated iron-cobalt hybrid hemoglobins (Hbs), (alpha Co-O2 beta Fe-O2)2 and (alpha Fe-O2 beta Co-O2)2, were studied by electron spin echo envelope modulation (ESEEM) spectroscopy in order to measure (i) electron-nuclear hyperfine and nuclear quadrupole coupling to the N epsilon of the proximal histidyl imidazol...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00020a036
更新日期：1995-05-23 00:00:00
abstract：:The contribution of backbone hydrogen bonds in alpha-helices to the overall stability of a protein has been examined experimentally by replacing several backbone amide linkages in alpha-helix 39-50 of T4 lysozyme with ester linkages. T4 lysozyme variants wherein the backbone amide bonds between residues Ser38 and Leu3...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9707685
更新日期：1997-09-23 00:00:00
abstract：:The proton nuclear magnetic resonance spectrum of human adult deoxyhemoglobin in D2O in the region from 6 to 20 ppm downfield from the proton resonance of residual water shows a number of hyperfine shifted proton resonances that are due to groups on or near the alpha and beta hemes. The sensitivity of these resonances...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00590a031
更新日期：1979-11-13 00:00:00
abstract：:By use of six highly purified exoglycosidases with well-defined specificity, the oligosaccharide units of human plasma beta 2-glycoprotein I (beta 2I) were modified by sequential enzymatic degradation. The released monosaccharides (NeuAc, Gal, GlcNAc, and Man) were quantified, and the carbohydrate compositions of the ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00478a020
更新日期：1990-07-03 00:00:00
abstract：:VSTx1 is a voltage sensor toxin from the spider Grammostola spatulata that inhibits KvAP, an archeabacterial voltage-activated K(+) channel whose X-ray structure has been reported. Although the receptor for VSTx1 and the mechanism of inhibition are unknown, the sequence of the toxin is related to hanatoxin (HaTx) and ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0477034
更新日期：2005-04-26 00:00:00
abstract：:Phytochromes are widespread red/far-red photosensory proteins well known as critical regulators of photomorphogenesis in plants. It is often assumed that natural selection would have optimized the light sensing efficiency of phytochromes to minimize nonproductive photochemical deexcitation pathways. Surprisingly, the ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi500108s
更新日期：2014-05-06 00:00:00
abstract：:The vibrations of a water molecule in the water-oxidizing complex (WOC) of photosystem II were detected for the first time using Fourier transform infrared (FTIR) spectroscopy. In a flash-induced FTIR difference spectrum upon the S(1)-to-S(2) transition, a pair of positive and negative bands was observed at 3618 and 3...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi001040i
更新日期：2000-09-12 00:00:00
abstract：:Factor VIII (fVIII) is synthesized as a single chain having a domainal sequence A1-A2-B-A3-C1-C2. Analysis of the proteolyic cleavage of fVIII by thrombin by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) identifies three fragments designated fVIIIA1, fVIIIA2, and fVIIIA3-C1-C2 with fragment(s) d...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00428a038
更新日期：1989-01-24 00:00:00
abstract：:The 24-kDa subunit of mitochondrial NADH-ubiquinone reductase (complex I) is an iron-sulfur protein that is present in the flavoprotein or NADH dehydrogenase II subcomplex. It is a nuclear gene product and is imported into the organelle. A group of human patients with mitochondrial myopathy have been shown to have red...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00434a021
更新日期：1989-04-18 00:00:00
abstract：:A covalent dimer of Saccharomyces cerevisiae iso-1 cytochrome c is stabilized by an interchain disulfide bond involving the cysteine residue penultimate to the C-terminus. The individual chains in the dimer appear to retain the tertiary structural features characteristic for monomeric cytochrome c albeit with some per...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00335a011
更新日期：1985-07-02 00:00:00
abstract：:Thermococcus litoralis 4-alpha-glucanotransferase (TLGT) belongs to family 57 of glycoside hydrolases and catalyzes the disproportionation and cycloamylose synthesis reactions. Family 57 glycoside hydrolases have not been well investigated, and even the catalytic mechanism involving the active site residues has not be...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi011017c
更新日期：2001-10-16 00:00:00
