Abstract：
:Several basic proteins, including the ubiquitous HU proteins, serve histone-like functions in prokaryotes. Significant sequence conservation exists between HU homologues; yet binding sites varying from 9 to 37 bp have been reported. TF1, an HU homologue with a 37 bp binding site that is encoded by the Bacillus subtilis bacteriophage SPO1, binds with nM affinity to DNA that contains 5-hydroxymethyluracil (hmU) in place of thymine and to T-containing DNA with loops. We evaluated the contribution of three conserved lysines to specifying the length of the binding site and show that Lys3 is critical for maintaining a long binding site in T-containing DNA: A mutant protein in which Lys3 is replaced with Gln(TF1-K3Q) is completely deficient in forming a stable complex. The affinity for 37 bp hmU-containing DNA is also reduced, from approximately 3 nM for wild-type TF1 to approximately 90 nM for TF1-K3Q. The decrease in affinity of TF1-K3Q for hmU-containing DNA > or = 25 bp suggests that Lys3 contacts DNA 8-9 bp distal to the sites of kinking. We propose that Lys3 forms an internal saltbridge to Asp26 in HU homologues characterized by shorter binding sites and that its surface exposure, and hence a longer binding site, may correlate with absence of this aspartate.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Grove A,Saavedra TCdoi
10.1021/bi016095esubject
Has Abstractpub_date
2002-06-18 00:00:00pages
7597-603issue
24eissn
0006-2960issn
1520-4995pii
bi016095ejournal_volume
41pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:The inflammatory mediator nitric oxide (NO*) promotes apoptotic cell death based on morphological evidence, accumulation of the tumor suppressor p53, caspase-3 activation, and DNA fragmentation in RAW 264.7 macrophages. Since nitrosothiols may actually be the predominant form of biologically active NO* in vivo, we use...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi982292a
更新日期：1999-02-23 00:00:00
abstract：:The (beta alpha)8 (or "TIM")-barrel protein phosphoribosylanthranilate isomerase from Saccharomyces cerevisiae was cleaved between the sixth and seventh beta alpha module to test the capacity of the resulting fragments to adopt native format autonomously. The fragments, which were expressed from separate coding sequen...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00129a010
更新日期：1992-04-14 00:00:00
abstract：:Heme-copper oxidases are membrane-bound proteins that catalyze the reduction of O(2) to H(2)O, a highly exergonic reaction. Part of the free energy of this reaction is used for pumping of protons across the membrane. The ba(3) oxidase from Thermus thermophilus presumably uses a single proton pathway for the transfer o...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi300132t
更新日期：2012-06-05 00:00:00
abstract：:Three hybridomas secreting monoclonal antibodies, HH1, HH2, and HH3, defining different difucosyl A structures (ALeb or ALey), have been established. Antibody HH1 (IgG2a) reacts specifically with the difucosyl A structure irrespective of a type 1 or type 2 chain, while antibody HH2 (IgG3) reacts exclusively with the d...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00343a024
更新日期：1985-10-22 00:00:00
abstract：:A new actinoleukin-like antitumor antibiotic, BBM-928A, has been shown to interact with isolated DNA molecules. BBM-928A contains two substituted quinolines linked by a cyclic decapeptide. Quenching effects of the covalently closed superhelical PM2 DNA on the BBM-928A fluorescence revealed a strong interaction with an...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00565a012
更新日期：1980-11-25 00:00:00
abstract：:The peptide hormone bradykinin exerts important biological functions by binding to and activating bradykinin B2 receptors. B2 receptors belong to the seven transmembrane domain (7TM) receptor family. Cloning of the cDNA sequences for the rat, human, and mouse bradykinin B2 receptor revealed several in-frame AUG triple...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9601060
更新日期：1996-06-11 00:00:00
abstract：:Initiation of RNA synthesis by Bacillus subtilis RNA polymerase (sigma-43) has been examined at two early promoters of phage phi 29: the A2 promoter, which is a weak promoter, and the G2 promoter, which is a strong promoter. The delta subunit of the polymerase inhibits the rate of initiation at A2, but not G2. In addi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00399a028
更新日期：1987-12-15 00:00:00
abstract：:DNA photolyases catalyze the splitting of the cyclobutane ring joining the two dihydropyrimidines of a pyrimidine dimer by a photoinduced electron-transfer reaction. Previous studies concluded that photolyase repairs only the cis-syn form of the eight stereoisomers of the cyclobutane pyrimidine dimer (Pyr[ ]Pyr). In t...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00079a001
更新日期：1993-07-20 00:00:00
abstract：:During initiation of minus-strand synthesis by HIV-1 reverse transcriptase, a 3'-DNA-RNA-5' junction is formed involving the 3'-end of tRNAlys,3. The HIV-RT-associated RNase H cleaves the RNA template strand specifically, opposite the newly synthesized DNA strand. We have determined the crystal structure at 1.9 A reso...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi981152y
更新日期：1998-09-01 00:00:00
abstract：:Several enzymatic and chemical reagents were used to probe the secondary structure of Saccharomyces cerevisiae nuclear RNase P RNA in the presence and absence of its protein components. Double-stranded regions were detected with RNase V1 and single-stranded regions with RNase ONE (Escherichia coli RNase I). Nucleotide...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00173a022
更新日期：1994-02-22 00:00:00
abstract：:We report here that polyamide nucleic acid (PNA) as well as a polyamide nucleic acid-DNA chimera complementary to the primer binding site of the HIV-1 genome can completely block priming by tRNA3Lys and consequently the in vitro initiation of reverse transcription by HIV-1 RT. Conventional heating and cooling is not r...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi972197m
更新日期：1998-01-20 00:00:00
abstract：:The calcitonin gene-related peptide (CGRP) receptor is a heterodimer of two membrane proteins: calcitonin receptor-like receptor (CLR) and receptor activity-modifying protein 1 (RAMP1). CLR is a class B G-protein-coupled receptor (GPCR), possessing a characteristic large amino-terminal extracellular domain (ECD) impor...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi901848m
更新日期：2010-03-09 00:00:00
abstract：:The Xenopus borealis somatic 5S ribosomal RNA gene was used as a model system to determine the mutual effects of nucleosome folding and formation of ultraviolet (UV) photoproducts (primarily cis-syn cyclobutane pyrimidine dimers, or CPDs) in chromatin. We analyzed the preferred rotational and translational settings of...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi991771m
更新日期：2000-01-25 00:00:00
abstract：:Human DNA polymerase kappa (pol kappa) has a sequence significantly homologous with that of Escherichia coli DNA polymerase IV (pol IV). We used a truncated form of human pol kappa (pol kappaDeltaC) and full-length pol IV to explore the miscoding properties of these enzymes. Oligodeoxynucleotides, modified site-specif...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi010702g
更新日期：2001-12-18 00:00:00
abstract：:In mammals, numerous precursors of antibacterial peptides with unrelated sequences share a similar prosequence of 94-114 residues, termed the cathelin-like domain. The cathelin-like domain of protegrin-3 (ProS) was overexpressed in Escherichia coli and uniformly labeled with (15)N or (15)N and (13)C, and its three-dim...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi027133c
更新日期：2003-04-29 00:00:00
abstract：:The effects of several guanine nucleotide analogues on (Na+,K+)-ATPase activity of membranes isolated from several tissues were analyzed to determine if a G-protein might be involved in the hormonal regulation of the (Na+,K+)-ATPase. Submillimolar concentrations of GTP gamma S, but not GMPPNP, inhibit rat skeletal mus...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00241a014
更新日期：1991-07-09 00:00:00
abstract：:1-Bromovinyl (I), Z-2-bromovinyl (II), 1,2-dibromoethyl (III), and a series of 4-(halomethyl)-2-nitrophenyl (IVa-c) diethyl phosphate esters were examined as substrates and mechanism-based inhibitors for the bacterial phosphotriesterase. All of these compounds were found to act as substrates for the enzyme. Inhibitor ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi970680r
更新日期：1997-07-22 00:00:00
abstract：:The light-driven enzyme NADPH:protochlorophyllide oxidoreductase (POR) catalyzes the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), a key regulatory step in the chlorophyll biosynthesis pathway. As POR is light activated, it allows intermediates in the reaction pathway to be observed by initiat...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0268448
更新日期：2003-01-21 00:00:00
abstract：:In fosfomycin biosynthesis, the hydrolysis of cytidylyl ( S)-2-hydroxypropylphosphonate [( S)-HPP-CMP] to afford ( S)-HPP is the only uncharacterized step. Because FomD is an uncharacterized protein with a DUF402 domain that is encoded in the fosfomycin biosynthetic gene cluster, FomD was hypothesized to be responsibl...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.8b00690
更新日期：2018-08-14 00:00:00
abstract：:The single-stranded packaged genome (ssDNA) of bacteriophage phi X174 is shown by Raman spectroscopy to lack both the ordered phosphodiester backbone and base stacking, which are demonstrated for unpackaged, protein-free ssDNA. In solutions of moderate ionic strength, unpackaged ssDNA contains 36 +/- 7% of deoxyribosy...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00234a004
更新日期：1991-05-21 00:00:00
abstract：:The structures of beta class carbonic anhydrases (beta-CAs) determined so far fall into two distinct subclasses based on the observed coordination of the catalytic zinc (Zn2+) ion. The subclass of beta-CAs that coordinate Zn2+ tetrahedrally with four protein-derived ligands is represented by the structures of ortholog...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi052272q
更新日期：2006-04-11 00:00:00
abstract：:Acyl-CoA:cholesterol O-acyltransferase (EC 2.3.1.26) (ACAT) catalyzes the intracellular synthesis of cholesteryl esters from cholesterol and fatty acyl-CoA at neutral pH. Despite the probable pathophysiologic role of ACAT in vascular cholesteryl ester accumulation during atherogenesis, its mechanism of action and its ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00419a025
更新日期：1988-09-20 00:00:00
abstract：:Factor V and factor Va binding to single bilayer phospholipid vesicles was investigated by light-scattering intensity measurements. This technique allows the measurement of free and phospholipid-bound protein concentrations from which equilibrium constants can be obtained. As controls, the Ca2+-dependent phospholipid ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00587a023
更新日期：1979-10-02 00:00:00
abstract：:The structure of PsbQ, one of the three main extrinsic proteins associated with the oxygen-evolving complex (OEC) of higher plants and green algae, is examined by Fourier transform infrared (FTIR) and circular dichroic (CD) spectroscopy and by computational structural prediction methods. This protein, together with tw...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi026575l
更新日期：2003-02-04 00:00:00
abstract：:Methods were developed for isolation of bovine cardiac titin in the apparently full-sized T1 form. The pure protein could be obtained either in the denatured state after chromatography of myofibril extracts on Sephacryl S-1000 or in the native state using hydroxylapatite chromatography. Titin-specific chicken polyclon...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00193a012
更新日期：1994-07-12 00:00:00
abstract：:Adenosine 5'-phosphosulfate (APS) kinase catalyzes the second reaction in the two-step conversion of inorganic sulfate to 3'-phosphoadenosine 5'-phosphosulfate (PAPS). This report presents the 2.0 A resolution crystal structure of ligand-free APS kinase from the filamentous fungus, Penicillium chrysogenum. The enzyme ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9924157
更新日期：2000-02-22 00:00:00
abstract：:A series of antisense oligonucleotides (ASOs) were synthesized and tested to define the best target sites within an RNA transcript of collagen for effective inhibition of expression. The test system consisted of mouse NIH 3T3 fibroblasts that were stably transfected with a human minigene for procollagen I so that the ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00202a024
更新日期：1994-09-13 00:00:00
abstract：:Diethyl pyrocarbonate inhibited diaphorase activity of ferredoxin-NADP+ oxidoreductase with a second-order rate constant of 2 mM-1 X min-1 at pH 7.0 and 20 degrees C, showing a concomitant increase in absorbance at 242 nm due to formation of carbethoxyhistidyl derivatives. Activity could be restored by hydroxylamine, ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00294a031
更新日期：1983-12-06 00:00:00
abstract：:The disulfide structure of sillucin, a highly knotted, cysteine-rich, antimicrobial peptide, isolated from Rhizomucor pusillus, has been determined to be Cys2--Cys7, Cys12--Cys24, Cys13--Cys30, and Cys14--Cys21 by disulfide mass mapping based on partial reduction and CN-induced cleavage enabled by cyanylation. The den...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi002229x
更新日期：2001-04-17 00:00:00
abstract：:The toll that Streptococcus pneumoniae exacts on the welfare of humanity is enormous. This organism claims the lives of approximately 3700 people daily, the majority of whom are children below the age of 5, and the situation could worsen due to the increasing incidence of pernicious, multiple-antibiotic-resistant stra...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi048075t
更新日期：2004-12-28 00:00:00
