Abstract:
:The structures of two RNA duplexes, whose sequences correspond to portions of the ColE1 plasmid copy control RNA I and RNA II, have been determined. Crystals containing the 18mers 5'-CA CCGUUGGUAGCGGUGC-3' and 5'-CACCGCUACCAACGGUGC-3' diffract to 1.20 A resolution while those containing the 19mers 5'-GCACCGUUGGUAGCGGUGC-3' and 5'-GCACCGCUACCAACGGUGC-3' diffract to 1.55 A resolution. Both duplexes are standard A form, with Watson-Crick base pairing throughout. Use of anisotropic atomic displacement factors in refinement of the 1.20 A structure dramatically improved refinement statistics, resulting in a final R(free) of 15.0% and a crystallographic R-factor of 11.6%. Perhaps surprisingly, these crystals of the 18 base pair RNA exhibit a 36-fold static disorder, resulting in a structure with a single sugar-phosphate backbone conformation and an averaged base composition at each residue. Since the sugar-phosphate backbone structure is identical in the 36 different nucleotides that are superimposed, there can be no sequence-dependent variation in the structure. The average ribose pucker amplitude is 45.8 degrees for the 18 base pair structure and 46.4 degrees for the 19 base pair structure; these values are respectively 19% and 20% larger than the average pucker amplitude reported from nucleoside crystal structures. A standard RNA water structure, based on analysis of the hydration of these crystal structures and that of the TAR RNA stem [Ippolito, J. A., and Steitz, T. A. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 9819-9824], has been derived, which has allowed us to predict water positions in lower resolution RNA crystal structures. We report a new RNA packing motif, in which three pro-S(p) phosphate oxygens interact with an ammonium ion.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Klosterman PS,Shah SA,Steitz TAdoi
10.1021/bi9912793subject
Has Abstractpub_date
1999-11-09 00:00:00pages
14784-92issue
45eissn
0006-2960issn
1520-4995pii
bi9912793journal_volume
38pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Well-ordered multilamellar arrays of liquid-crystalline phosphatidylcholine and equimolar phosphatidylcholine-cholesterol bilayers have been formed in the nonaqueous solvents formamide and 1,3-propanediol. The organization of these bilayers and the interactions between apposing bilayer surfaces have been investigated ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00445a053
更新日期:1989-09-19 00:00:00
abstract::Sulfite oxidase (SO) catalyzes the physiologically critical conversion of sulfite to sulfate. Enzymatic activity is dependent on the presence of the metal molybdenum complexed with a pyranopterin-dithiolene cofactor termed molybdopterin. Comparison of the amino acid sequences of SOs from a variety of sources has ident...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi1001954
更新日期:2010-05-11 00:00:00
abstract::Heme catabolism is an important biochemical process that many bacterial pathogens utilize to acquire iron. However, tetrapyrrole catabolites can be reactive and often require further processing for transport out of the cell or conversion to another useful cofactor. In previous work, we presented in vitro evidence of a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b01099
更新日期:2017-02-14 00:00:00
abstract::Classical strategies for structure analysis of proteins interacting with a lipid phase typically correlate ensemble secondary structure content measurements with changes in the spectroscopic responses of localized aromatic residues or reporter molecules to map regional solvent environments. Deep-UV resonance Raman (DU...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi200596w
更新日期:2011-08-02 00:00:00
abstract::The Escherichia coli single-strand binding (SSB) protein is an essential protein involved in DNA replication, recombination, and repair processes. The tetrameric protein binds to ss nucleic acids in a number of different binding modes in vitro. These modes differ in the number of nucleotides occluded per SSB tetramer ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00141a029
更新日期:1992-07-07 00:00:00
abstract::Zinc finger nucleases (ZFNs) have been used to direct precise modifications of the genetic information in living cells at high efficiency. An important consideration in the design of ZFNs is the number of zinc fingers that are required for efficient and specific cleavage. We examined dimeric ZFNs composed of [1]+[1], ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi200393g
更新日期:2011-06-07 00:00:00
abstract::Halorhodopsin from Natronomonas pharaonis (NpHR) acts an inward-directed, light-driven chloride pump and forms a homotrimer. To evaluate effect of trimeric assembly, that is, intermolecular interaction, on the control or modulation of light-driven chloride pumping activity of individual HRs, it is important to underst...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi901380c
更新日期:2009-12-29 00:00:00
abstract::A debilitating complication of long-term hemodialysis is the deposition of beta-2-microglobulin (beta2m) as amyloid plaques in the joint space. We have recently shown that Cu(2+) can be a contributing, if not causal, factor at concentrations encountered during dialysis therapy. The basis for this effect is destabiliza...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi025944a
更新日期:2002-08-27 00:00:00
abstract::The actin cytoskeleton carries out cellular functions, including division, migration, adhesion, and intracellular transport, that require a variety of actin binding proteins, including myosins. Our focus here is on class II nonmuscle myosin isoforms, NMIIA, NMIIB, and NMIIC, and their regulation by the actin binding p...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi500162z
更新日期:2014-06-24 00:00:00
abstract::Vertical fluctuations of the terminal methyl groups of stearic acid acyl chains toward the surface of dimyristoylphosphatidylcholine (DMPC) bilayers have been investigated by using spin-label electron-electron double-resonance ( ELDOR ) methodology. Spin-label pairs consisting of two populations of stearic acid spin-l...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00305a032
更新日期:1984-05-08 00:00:00
abstract::The positions, with respect to the plasma membrane, of lysine 905, contained in the peptide QRKIVE, and of lysine 1012, contained in the carboxy-terminal peptide, RPGGWVEKETYY, of ovine Na+/K(+)-transporting ATPase have been reported to be cytoplasmic and extracytoplasmic, respectively [Bayer, R. (1990) Biochemistry 2...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00062a012
更新日期:1993-03-23 00:00:00
abstract::The kinetics of the interconversions of the subgel and gel phases in dipalmitoylphosphatidylcholine have been studied by using differential dilatometry, differential scanning calorimetry (DSC), and neutral buoyancy centrifugation as a function of incubation temperature and deuteriation of the solvent. As seen by other...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00388a016
更新日期:1987-07-14 00:00:00
abstract::Steroid receptors define a family of ligand-activated transcription factors. Recent work has demonstrated that the receptors regulate distinct but overlapping gene networks, yet the mechanisms by which they do so remain unclear. We previously determined the microscopic binding energetics for progesterone receptor (PR)...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi2017156
更新日期:2012-01-24 00:00:00
abstract::The cyclic decapeptide antibiotic tyrocidine A was studied by two relatively new methods, viz., correlation proton magnetic resonance (pmr) spectroscopy and double-resonance difference pmr spectroscopy. The correlation method of spectral accumulation provided pmr spectra of good resolution, and in addition the signal-...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00673a032
更新日期:1975-01-28 00:00:00
abstract::The DNA binding of three platinum(II) intercalation reagents has been studied and found to depend upon base composition, the nature of the intercalator, and the ionic strength of the solvent medium. In 0.2 M NaCl, binding data for calf thymus DNA show the association constants to be approximately 10(4) M-1. The bindin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00593a003
更新日期:1979-12-25 00:00:00
abstract::Coupling of bovine carboxypeptidase A with diazotized 5-amino-1H-tetrazole increases esterase activity, decreases peptidase activity slightly, and modifies one tyrosyl residue. Subsequent nitration of the azoenzyme has no further effect on esterase activity, decreases peptidase activity markedly, and modifies a second...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00603a005
更新日期:1978-05-16 00:00:00
abstract::Recent studies have shown that there can be large differences in the stability of double and triple helical nucleic acid complexes, depending on whether RNA or DNA strands are involved. These differences have been attributed to structural differences in the sugar-phosphate backbone of these two polymers. However, sinc...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00012a031
更新日期:1995-03-28 00:00:00
abstract::Western blot analysis, using a polyclonal antibody to the 240-kDa endogenous inhibitor of the 20 S proteasome, revealed that the inhibitor is a component of the 26 S complex. Although isolated inhibitor displayed a single 40-kDa band on SDS-PAGE, the antibody detected a 55-kDa component in the 26 S proteasome complex....
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00163a001
更新日期:1992-12-08 00:00:00
abstract::The X-ray crystal structure of the complex of the B-DNA dodecamer CGCGAATTCGCG with the antitumor drug netropsin has been reexamined to locate the drug accurately for computer-based drug design. The optimum solution is with the drug centered in the AATT region of the minor groove, making three good bifurcated hydrogen...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00015a009
更新日期:1995-04-18 00:00:00
abstract::Human erythrocyte band 3 inhibits glycolytic enzymes, including aldolase, by binding these cytoplasmic enzymes at its N-terminus. Phosphorylation of Y8 disrupts inhibition, and there is evidence that in vivo glycolysis levels in erythrocytes are regulated in part by a phosphorylation/dephosphorylation signaling pathwa...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00051a005
更新日期:1995-12-26 00:00:00
abstract::Human prolactin (hPRL) binds two human prolactin receptor molecules, creating active heterotrimeric complexes. Receptors bind dissimilar hormone surfaces termed site 1 and site 2 in an obligate ordered process. We sought to map the functional epitopes in site 1 of hPRL. Extensive alanine mutagenesis (102 of the 199 re...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi101838s
更新日期:2011-03-01 00:00:00
abstract::BamA is an essential component of the β-barrel assembly machine (BAM) that is responsible for insertion and folding of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. BamA is an OMP itself, and its β-barrel transmembrane domain is thought to catalyze OMP insertion and folding, although the molecular...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.7b00281
更新日期:2017-06-20 00:00:00
abstract::A novel single polypeptide endopeptidase of 24 kDa (24k-endopeptidase) was purified with a yield of 300-400 microg/L from conditioned medium of a bacterial strain which was identified as a new species in the genus Chryseobacterium Sp. on the basis of its 16S rDNA sequence and DNA:DNA hybridizations. The NH(2)-terminal...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi992014r
更新日期:2000-01-18 00:00:00
abstract::Two distinct regions of angiogenin are critical for angiogenic activity: a catalytic site capable of cleaving RNA and a noncatalytic site, encompassing residues 60-68, which may bind to an endothelial cell-surface receptor [Hallahan, T. W., Shapiro, R., & Vallee, B. L. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 2222-222...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00149a036
更新日期:1992-09-01 00:00:00
abstract::R67 dihydrofolate reductase (DHFR), which catalyzes the NADPH dependent reduction of dihydrofolate to tetrahydrofolate, belongs to a type II family of R-plasmid encoded DHFRs that confer resistance to the antibacterial drug trimethoprim. Crystal structure data reveals this enzyme is a homotetramer that possesses a sin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi034643d
更新日期:2003-09-16 00:00:00
abstract::The N-acyl- l-homoserine lactone hydrolases (AHL lactonases) have attracted considerable attention because of their ability to quench AHL-mediated quorum-sensing pathways in Gram-negative bacteria and because of their relation to other enzymes in the metallo-beta-lactamase superfamily. To elucidate the detailed cataly...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi8003704
更新日期:2008-07-22 00:00:00
abstract::Bacterial bioluminescence is a phenomenon resulting from the reaction of a two-component FMN-dependent aldehyde monooxygenase system, which comprises a bacterial luciferase and a flavin reductase. Bacterial luciferase (LuxAB) is one of the most extensively investigated two-component monooxygenases, while its reductase...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi1009985
更新日期:2010-11-02 00:00:00
abstract::The Plasmodium falciparum malarial parasite genome appears to encode one and only one phosphatidylinositol 3'-kinase (PI3K), and sequence analysis suggests that the enzyme is a "class III"- or "Vps34"-type PI3K. PfVps34 has generated excitement as a possible druggable target and potentially a key target of artemisinin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.7b00416
更新日期:2017-08-22 00:00:00
abstract::Factor XIIIa (a2') is a homodimeric transglutaminase that is formed via limited alpha-thrombin-catalyzed proteolysis of the platelet (a2) or plasma (a2b2) factor XIII zymogen in a reaction that results in proteolytic removal of a 37-aminoacyl residue peptide from the N-terminus of the a chains and exposure of the acti...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00117a017
更新日期:1992-01-21 00:00:00
abstract::The stereoselectivity of the adenosine cyclic 3',5'-phosphate (cAMP) binding sites on the regulatory subunit of the type II bovine cardiac muscle cAMP-dependent protein kinase was investigated by examining the interactions of (Rp)- and (Sp)-adenosine cyclic 3',5'-phosphorothioates (cAMPS) with these sites. While activ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00261a028
更新日期:1982-08-31 00:00:00