Primary structure of the second largest subunit of human RNA polymerase II (or B).

abstract：:The variety of biogenesis pathways for small nucleolar RNAs (snoRNAs) reflects the diversity of their genomic organization. We have searched for yeast snoRNAs which are affected by the depletion of the yeast ortholog of bacterial RNase III, Rnt1. In a yeast strain inactivated for RNT1, almost half of the snoRNAs teste...

journal_title：Journal of molecular biology

authors： Chanfreau G,Legrain P,Jacquier A

更新日期：1998-12-11 00:00:00

abstract：:Abasic lesions are common mutagenic or cytotoxic DNA damages. Ape1 is the major human apurinic/apyrimidinic (AP) endonuclease and initiates repair of abasic sites by catalyzing strand cleavage at the lesion. I show here that Ape1 single-stranded (ss) AP site incision activity prefers 0.5 mM or 2 mM MgCl(2) and low con...

journal_title：Journal of molecular biology

authors： Wilson DM 3rd

更新日期：2005-02-04 00:00:00

abstract：:We have studied the use of nearest-neighbor classifiers to predict the secondary structure of proteins. The nearest-neighbor rule states that a test instance is classified according to the classifications of "nearby" training examples from a database of known structures. In the context of secondary structure predictio...

journal_title：Journal of molecular biology

authors： Yi TM,Lander ES

更新日期：1993-08-20 00:00:00

abstract：:A mannose-specific agglutinin, isolated from garlic bulbs, has been crystallized in the presence of a large excess of alpha-d-mannose, in space group C2 and cell dimensions, a=203.24, b=43.78, c=79.27 A, beta=112.4 degrees, with two dimers in the asymmetric unit. X-ray diffraction data were collected up to a nominal r...

journal_title：Journal of molecular biology

authors： Chandra NR,Ramachandraiah G,Bachhawat K,Dam TK,Surolia A,Vijayan M

更新日期：1999-01-22 00:00:00

abstract：:CloQ is an aromatic prenyltransferase from the clorobiocin biosynthetic pathway of Streptomyces roseochromogenes var. oscitans. It is involved in the synthesis of the prenylated hydroxybenzoate moiety of the antibiotic, specifically catalyzing the attachment of a dimethylallyl moiety to 4-hydroxyphenylpyruvate. Herein...

journal_title：Journal of molecular biology

authors： Metzger U,Keller S,Stevenson CE,Heide L,Lawson DM

更新日期：2010-12-10 00:00:00

abstract：:We have previously reported the structures of the native holo and substrate-bound forms of LL-diaminopimelate aminotransferase from Arabidopsis thaliana (AtDAP-AT). Here, we report the crystal and molecular structures of the LL-diaminopimelate aminotransferase from Chlamydia trachomatis (CtDAP-AT) in the apo-form and ...

journal_title：Journal of molecular biology

authors： Watanabe N,Clay MD,van Belkum MJ,Fan C,Vederas JC,James MN

更新日期：2011-08-19 00:00:00

abstract：:We have solved the crystal structure of FRase I, the major NAD(P)H:FMN oxidoreductase of Vibrio fischeri, by the multiple isomorphous replacement method (MIR) at 1.8 A resolution with the conventional R factor of 0.187. The crystal structure of FRase I complexed with its competitive inhibitor, dicoumarol, has also bee...

journal_title：Journal of molecular biology

authors： Koike H,Sasaki H,Kobori T,Zenno S,Saigo K,Murphy ME,Adman ET,Tanokura M

更新日期：1998-07-10 00:00:00

abstract：:The ribosomal protein L30 from yeast Saccharomyces cerevisiae auto-regulates its own synthesis by binding to a structural element in both its pre-mRNA and its mRNA. The three-dimensional structures of L30 in the free (f L30) and the pre-mRNA bound (b L30) forms have been solved by nuclear magnetic resonance spectrosco...

journal_title：Journal of molecular biology

authors： Mao H,Williamson JR

更新日期：1999-09-17 00:00:00

abstract：:Herpes simplex viruses (HSVs) are human pathogens that establish lytic and latent infections. Reactivation from latency occurs intermittently, which represents a lifelong source of recurrent infection. In this complex process, HSV triggers and neutralizes innate immunity. Therefore, a dynamic equilibrium between HSV a...

journal_title：Journal of molecular biology

authors： Ma Y,He B

更新日期：2014-03-20 00:00:00

abstract：:Phenylalanyl-tRNA synthetase (EC 6.1.1.20) from the extreme thermophile Thermus thermophilus HB8 has been isolated and crystallized. The enzyme was found to consist of two types of subunits with molecular masses 38 X 10(3) (alpha) and 94 X 10(3) (beta) and is likely to be a tetrameric protein with a molecular mass of ...

journal_title：Journal of molecular biology

authors： Chernaya MM,Korolev SV,Reshetnikova LS,Safro MG

更新日期：1987-12-05 00:00:00

abstract：:Large crystals of probable amylase/protease inhibitor-B have been grown at room temperature from ammonium sulfate solution. The crystals grow within five days to dimensions of 0.6 mm x 0.6 mm x 0.6 mm. They diffract to at least 1.7 A upon exposure to synchrotron X-rays. The crystals belong to the space group P4(1)2(1)...

journal_title：Journal of molecular biology

authors： Hwang KY,Kim KK,Min K,Eom SH,Yu YG,Kim S,Sweet RM,Suh SW

更新日期：1993-01-05 00:00:00

abstract：:The tetracycline analog 9-(N, N-dimethylglycylamido)-6-demethyl-6-deoxy-tetracycline (9glyTc) belongs to a new group of tetracyclines called glycylcyclines. They are strong antibiotics showing reduced sensitivity against the major tetracycline resistance mechanisms. We have determined the crystal structure of 9glyTc i...

journal_title：Journal of molecular biology

authors： Orth P,Schnappinger D,Sum PE,Ellestad GA,Hillen W,Saenger W,Hinrichs W

更新日期：1999-01-15 00:00:00

abstract：:Bloom syndrome protein (BLM) is one of five human RecQ helicases that participate in DNA metabolism. RecQ C-terminal (RQC) domain is the main DNA binding module of BLM and specifically recognizes G-quadruplex (G4) DNA structures. Because G4 processing by BLM is essential for regulating replication and transcription, b...

journal_title：Journal of molecular biology

authors： Lee S,Lee AR,Ryu KS,Lee JH,Park CJ

更新日期：2019-02-15 00:00:00

abstract：:In the filamentous fungus Podospora anserina, the unavoidable phenomenon of senescence is associated with specific mitochondrial rearrangements and particularly with the amplification of some regions of the mitochondrial chromosome. Mechanisms responsible for these rearrangements are still unknown. The implication in ...

journal_title：Journal of molecular biology

authors： Sainsard-Chanet A,Begel O,Belcour L

更新日期：1993-11-05 00:00:00

abstract：:The X-ray crystal structure of a catalytic-site mutant EQ208 [Glu208-->Gln] of alpha-amylase from Bacillus subtilis cocrystallized with maltopentaose (G5) and acarbose has been determined by multiple isomorphous replacement at 2.5 A resolution. Restrained crystallographic refinement has resulted in an R-factor of 19.8...

journal_title：Journal of molecular biology

authors： Fujimoto Z,Takase K,Doui N,Momma M,Matsumoto T,Mizuno H

更新日期：1998-03-27 00:00:00

abstract：:Previously we have shown that nuclear extracts from mouse cells contain a heterogeneous group of polypeptides (p65, p80, p90, p100) which form distinct DNA-protein complexes on the 18 base-pair sequence element (termed Sal-box), which constitutes the murine rDNA transcription termination signal. These distinct protein...

journal_title：Journal of molecular biology

authors： Smid A,Finsterer M,Grummt I

更新日期：1992-10-05 00:00:00

abstract：:Many proteins have small-molecule binding pockets that are not easily detectable in the ligand-free structures. These cryptic sites require a conformational change to become apparent; a cryptic site can therefore be defined as a site that forms a pocket in a holo structure, but not in the apo structure. Because many p...

journal_title：Journal of molecular biology

authors： Cimermancic P,Weinkam P,Rettenmaier TJ,Bichmann L,Keedy DA,Woldeyes RA,Schneidman-Duhovny D,Demerdash ON,Mitchell JC,Wells JA,Fraser JS,Sali A

更新日期：2016-02-22 00:00:00

abstract：:Aminoacyl-tRNA synthetases are validated molecular targets for anti-infective drug discovery because of their essentiality in protein synthesis. Thanks to genome sequencing, it is now possible to systematically study aminoacyl-tRNA synthetases from human eukaryotic parasites as putative targets for novel drug discover...

journal_title：Journal of molecular biology

authors： Crepin T,Peterson F,Haertlein M,Jensen D,Wang C,Cusack S,Kron M

更新日期：2011-01-28 00:00:00

abstract：:Native state 1H NMR resonance assignments for 125 of the 129 residues of equine lysozyme have enabled measurement of the hydrogen exchange kinetics for over 60 backbone amide and three tryptophan indole hydrogen atoms in the native state. Native holo equine lysozyme hydrogen exchange protection factors are as large as...

journal_title：Journal of molecular biology

authors： Morozova-Roche LA,Arico-Muendel CC,Haynie DT,Emelyanenko VI,Van Dael H,Dobson CM

更新日期：1997-05-23 00:00:00

abstract：:The binding of tryptophan repressor (TrpR) to its operators was examined quantitatively using in vitro and in vivo methods. DNA sequence requirements for 1:1 and tandem 2:1 (TrpR:DNA) binding in various sequence contexts were studied. The results indicate that the optimal half-site sequence for recognition by one heli...

journal_title：Journal of molecular biology

authors： Yang J,Gunasekera A,Lavoie TA,Jin L,Lewis DE,Carey J

更新日期：1996-04-26 00:00:00

abstract：:The mini-chromosome maintenance (MCM) complex is the presumptive replicative helicase in archaea and eukaryotes. In archaea, the MCM is a homo-multimer, in eukaryotes a heterohexamer composed of six related subunits, MCM 2-7. Biochemical studies using naked DNA templates have revealed that archaeal MCMs and a sub-comp...

journal_title：Journal of molecular biology

authors： Marsh VL,McGeoch AT,Bell SD

更新日期：2006-04-14 00:00:00

abstract：:Restriction fragments of bacteriophage lambda DNA corresponding to the major leftward transcription unit were purified, denatured to form single-stranded DNA, self-annealed, and examined by electron microscopy. Three intrastrand stem and loop secondary structures were observed reproducibly and the locations of the pai...

journal_title：Journal of molecular biology

authors： Edlind TD,Cooley TE,Richards SH,Ihler GM

更新日期：1984-11-05 00:00:00

abstract：:Bleomycin (Bm)-binding protein, designated BLMA, which is a Bm resistance determinant from Bm-producing Streptomyces verticillus, was crystallized in a form suitable for X-ray diffraction analysis. The diffraction intensity data were collected up to a resolution of 1.5 A with a merging R-value of 0.054 at a completene...

journal_title：Journal of molecular biology

authors： Kawano Y,Kumagai T,Muta K,Matoba Y,Davies J,Sugiyama M

更新日期：2000-01-28 00:00:00

abstract：:DNA methyltransferases flip their target base out of the DNA helix. Here, we have investigated base flipping by wild-type EcoRV DNA methyltransferase (M.EcoRV) and five M.EcoRV variants (D193A, Y196A, S229A, W231R and Y258A). These variants bind to DNA and S-adenosylmethionine but have a severely reduced catalytic eff...

journal_title：Journal of molecular biology

authors： Jeltsch A,Roth M,Friedrich T

更新日期：1999-01-22 00:00:00

abstract：:The high resolution structures of bovine pancreatic trypsin inhibitor refined in two distinct crystal forms have been compared. One of the structures was a result of new least-squares X-ray refinement of data from crystal form I, while the other was the joint X-ray/neutron structure of crystal form II. After superposi...

journal_title：Journal of molecular biology

authors： Wlodawer A,Deisenhofer J,Huber R

更新日期：1987-01-05 00:00:00

abstract：:Crystals of the mouse major urinary protein (MUP) and rat alpha-2u globulin (AMG) have been grown from solutions of polyethylene glycol 3350 and CdCl2, respectively. The crystals differ both in their morphologies and space groups but have very similar unit cell sizes. AMG crystallized in P2(1) (a = 56.6 A, b = 103.8 A...

journal_title：Journal of molecular biology

authors： Böcskei Z,Findlay JB,North AC,Phillips SE,Somers WS,Wright CE,Lionetti C,Tirindelli R,Cavaggioni A

更新日期：1991-04-20 00:00:00

abstract：:Although LEDGF/p75 is believed to act as a cellular cofactor of lentiviral integration by tethering integrase (IN) to chromatin, there is no good in vitro model to analyze this functionality. We designed an AlphaScreen assay to study how LEDGF/p75 modulates the interaction of human immunodeficiency virus type 1 IN wit...

journal_title：Journal of molecular biology

authors： McNeely M,Hendrix J,Busschots K,Boons E,Deleersnijder A,Gerard M,Christ F,Debyser Z

更新日期：2011-07-29 00:00:00

abstract：:The structure of mucor pusillus pepsin (EC 3.4.23.6), the aspartic proteinase from Mucor pusillus, has been refined to a crystallographic R-factor of 16.2% at 2.0 A resolution. The positions of 2638 protein atoms, 221 solvent atoms and a sulphate ion have been determined with an estimated root-mean-square (r.m.s.) err...

journal_title：Journal of molecular biology

authors： Newman M,Watson F,Roychowdhury P,Jones H,Badasso M,Cleasby A,Wood SP,Tickle IJ,Blundell TL

更新日期：1993-03-05 00:00:00

abstract：:Thioredoxins are low-molecular-mass proteins that function as hydrogen carriers in DNA synthesis and in the transformation of sulfur metabolites. They also act as regulatory proteins in the light-dependent enzyme activation during photosynthesis. F-type thioredoxin from spinach chloroplasts, a monomeric protein of 113...

journal_title：Journal of molecular biology

authors： Génovésio-Taverne JC,Jetzer Y,Sauder U,Hohenester E,Hughet C,Jansonius JN,Gardet-Salvi L,Schürmann P

更新日期：1991-12-05 00:00:00

abstract：:We have analysed antigen-contacting residues and combining site shape in the antibody Fv and Fab crystal structures now available from the Protein Data Bank. Antigen-contacting propensities are presented for each antibody residue, allowing a new definition for the complementarity determining regions (CDRs) to be propo...

journal_title：Journal of molecular biology

authors： MacCallum RM,Martin AC,Thornton JM

更新日期：1996-10-11 00:00:00