Abstract:
:A DNA (cytosine)-5-methyltransferase from Haemophilus aegyptius (M.Hae III), which catalyzes methyl transfer from S-adenosyl-L-methionine to DNA, has been crystallized as a covalent complex with a suicide oligonucleotide substrate. Crystals of the co-complex were grown by vapor diffusion with hanging droplets, using polyethylene glycol 3500 as the precipitant. The crystals belong to the orthorhombic space group P2(1)2(1)2(1); the unit cell parameters are a = 57.6 A, b = 108.0 A, c = 155.8 A with two protein-DNA complexes in the asymmetric unit. Complete sets of native and derivative data have been collected to 2.7 A using a laboratory source.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Reinisch KM,Chen L,Verdine GL,Lipscomb WNdoi
10.1006/jmbi.1994.1319subject
Has Abstractpub_date
1994-05-13 00:00:00pages
626-9issue
4eissn
0022-2836issn
1089-8638pii
S0022-2836(84)71319-2journal_volume
238pub_type
杂志文章abstract::Current techniques for the prediction of side-chain conformations on a fixed backbone have an accuracy limit of about 1.0-1.5 A rmsd for core residues. We have carried out a detailed and systematic analysis of the factors that influence the prediction of side-chain conformation and, on this basis, have succeeded in ex...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.2001.4865
更新日期:2001-08-10 00:00:00
abstract::The majority of archaeal viral genes are of unknown function hindering our understanding of the virus life cycle and viral interactions with their host. Here, we first describe functional characterization of ORF131b (gp17) and ORF436 (gp18) of Sulfolobus islandicus rod-shaped virus 2 (SIRV2), both encoding proteins of...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2015.03.013
更新日期:2015-06-19 00:00:00
abstract::Evidence is presented for the participation of the P loop (nucleotides G2250-C2254) of 23 S rRNA in establishing the tertiary structure of the peptidyl transferase center. Single base substitutions were introduced into the P loop, which participates in peptide bond formation through direct interaction with the CCA end...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1998.2410
更新日期:1999-01-29 00:00:00
abstract::The two-domain, 325 residue outer membrane protein OmpA is one of the most abundant proteins of Escherichia coli, playing a role in the maintenance of the integrity of the cell surface. The N-terminal domain, consisting of about 170 amino acid residues, is embedded in the membrane, presumably in the form of a beta-bar...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1995.0403
更新日期:1995-07-28 00:00:00
abstract::The lumazine synthase/riboflavin synthase complex of Bacillus subtilis consists of an icosahedral capsid of 60 beta subunits enclosing a core of 3 alpha subunits. The preparation of reconstituted hollow capsids consisting of 60 beta subunits and their crystallization in a hexagonal (space group P6(3)22) and in a monoc...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(92)90105-s
更新日期:1992-06-20 00:00:00
abstract::The pathogenically important cholesterol-binding pore-forming bacterial "thiol-activated" toxins (TATs) are commonly believed to be monomeric in solution and to undergo a transition on membrane binding mediated by cholesterol to an oligomeric pore. We present evidence, gained through the application of a number of bio...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1998.2258
更新日期:1998-12-11 00:00:00
abstract::The structure of the recombinant (-) gamma-lactamase from an Aureobacterium species has been solved at 1.73A resolution in the cubic space group F23 with unit cell parameters a=b=c=240.6A. The trimeric enzyme has an alpha/beta hydrolase fold and closely resembles the cofactor free haloperoxidases. The structure has be...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2004.03.001
更新日期:2004-04-30 00:00:00
abstract::The HIV gp41 protein catalyzes fusion between viral and target cell membranes. Although the ~20-residue N-terminal fusion peptide (FP) region is critical for fusion, the structure of this region is not well characterized in large gp41 constructs that model the gp41 state at different times during fusion. This paper de...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2013.11.010
更新日期:2014-03-06 00:00:00
abstract::The development of electrostatic interactions during the folding of the N-terminal domain of the ribosomal protein L9 (NTL9) is investigated by pH-dependent rate equilibrium free energy relationships. We show that Asp8, among six acidic residues, is involved in non-native, electrostatic interactions with K12 in the tr...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2006.04.038
更新日期:2006-06-23 00:00:00
abstract::The use of carbohydrate-mimicking peptides to induce immune responses against surface polysaccharides of pathogenic bacteria offers a novel approach to vaccine development. Factors governing antigenic and immunogenic mimicry, however, are complex and poorly understood. We have addressed this question using the anti-li...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2009.03.057
更新日期:2009-05-15 00:00:00
abstract::The SH3 domain is a protein-protein interaction module commonly found in intracellular signaling and adaptor proteins. The SH3 domains of multiple endocytic proteins have been recently implicated in binding ubiquitin, which serves as a signal for diverse cellular processes including gene regulation, endosomal sorting,...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2007.07.074
更新日期:2007-10-12 00:00:00
abstract::Human kallikrein 5 (hK5) is a member of the tissue kallikrein family of serine peptidases. It has trypsin-like substrate specificity, is inhibited by metal ions, and is abundantly expressed in human skin, where it is believed to play a central role in desquamation. To further understand the interaction of hK5 with sub...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2007.08.042
更新日期:2007-11-02 00:00:00
abstract::RIG-I-like receptors (RLRs) are nucleic acid sensors that activate antiviral innate immune response. These molecules recognize diverse non-self RNA substrates and are antagonized by several viral inhibitors. We performed an evolutionary analysis of RLR genes (RIG-I, MDA5, and LGP2) in mammals. Results indicated that p...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2013.10.040
更新日期:2014-03-20 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
pub_type: 杂志文章,评审
doi:10.1016/j.jmb.2013.11.012
更新日期:2014-03-20 00:00:00
abstract::The clarification of the physico-chemical determinants underlying amyloid deposition is critical for our understanding of misfolding diseases. With this purpose we have performed a systematic all-atom molecular dynamics (MD) study of a series of single point mutants of the de novo designed amyloidogenic peptide STVIIE...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2005.03.081
更新日期:2005-06-10 00:00:00
abstract::Aquaporin-4 (AQP4) is the predominant water channel in the mammalian brain and an important drug target for treatment of cerebral edema, bipolar disorder and mesial temporal lobe epilepsy. We determined the AQP4 structure by electron crystallography of double-layered, two-dimensional (2D) crystals. The structure allow...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2005.10.081
更新日期:2006-01-27 00:00:00
abstract::Homologous mammalian proteins were subjected to an exhaustive search for residues that are critical to their structure/function. Error-prone polymerase chain reactions were used to generate random mutations in the genes of bovine pancreatic ribonuclease (RNase A) and human angiogenin, and a genetic selection based on ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2006.07.020
更新日期:2006-09-22 00:00:00
abstract::Domain swapping has been shown to be an important mechanism controlling multiprotein assembly and has been suggested recently as a possible mechanism underlying protein aggregation. Understanding oligomerization via domain swapping is therefore of theoretical and practical importance. By using a symmetrized structure-...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2005.06.062
更新日期:2005-09-09 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
pub_type: 杂志文章
doi:10.1006/jmbi.1993.1558
更新日期:1993-11-05 00:00:00
abstract::Hsp40-like co-chaperones are ubiquitous enzymes that stimulate the protein refolding activity of Hsp70 family chaperones. They are widespread in prokaryotic and eukaryotic systems. In bacteria, the best characterized co-chaperone is the Escherichia coli DnaJ protein. Many γ-proteobacteria encode a functional homologue...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2011.05.043
更新日期:2011-08-12 00:00:00
abstract::Intercellular communication via gap junction membrane channels cannot occur until two apposing hemichannels (connexons) meet and dock to form a sealed cell-cell conduit. In particular, an important question is how does the structure at the extracellular surface influence the molecular recognition of the two connexons....
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1997.1580
更新日期:1998-03-27 00:00:00
abstract::The PHD finger and the bromodomain are small protein domains that occur in many proteins associated with phenomena related to chromatin. The bromodomain has been shown to bind acetylated lysine residues on histone tails. Lysine acetylation is one of several histone modifications that have been proposed to form the bas...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2004.01.051
更新日期:2004-04-02 00:00:00
abstract::As a model to examine the local distribution of sequence variation within large arrays of tandemly repeated DNA in complex genomes, the long-range organization of alpha-satellite DNA from human chromosome 17 was investigated. Three individual chromosomes, representing different alpha-satellite haplotypes, were segrega...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/s0022-2836(05)80056-7
更新日期:1990-11-05 00:00:00
abstract::Muscle-specific kinase (MuSK) is a receptor tyrosine kinase expressed exclusively in skeletal muscle, where it is required for formation of the neuromuscular junction. MuSK is activated by agrin, a neuron-derived heparan sulfate proteoglycan. Here, we report the crystal structure of the agrin-responsive first and seco...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2006.09.019
更新日期:2006-12-01 00:00:00
abstract::We used spin-labeled nucleotide analogs and fluorescence spectroscopy to monitor conformational changes at the nucleotide-binding site of wild-type Dictyostelium discoideum (WT) myosin and a construct containing a single tryptophan at position F239 near the switch 1 loop. Electron paramagnetic resonance (EPR) spectros...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2009.12.035
更新日期:2010-03-05 00:00:00
abstract::XPB is a superfamily 2 helicase with a 3'-5' polarity. In eukaryotes, XPB is an integral subunit of the transcription factor TFIIH, which plays a dual role in DNA opening at RNA polymerase II promoters and in establishing the repair bubble around a DNA lesion in nucleotide excision repair. Eukaryotic XPB has only very...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2007.12.019
更新日期:2008-02-22 00:00:00
abstract::We have identified independently folding units, so called "foldons", from non-homologous proteins representing different folds. We applied simple statistical arguments in order to estimate the size of the foldon universe required to construct all foldable proteins. Various alignment procedures yield about 2600 foldons...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1997.1205
更新日期:1997-09-12 00:00:00
abstract::The mechanism of initiation of DNA replication in eukaryotic rolling- circle replicons is still poorly understood in molecular terms. Geminiviruses, a family of plant DNA viruses, which use this strategy during part of their replicative cycle, replicate in the nucleus and are amenable to molecular studies. Except for ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1999.2916
更新日期:1999-07-16 00:00:00
abstract::Prion diseases are assumed to be caused by the infectious isoform, PrPsc, of a single cellular surface protein, PrPc. PrPsc is an insoluble form of PrPc and is believed to possess a different three-dimensional fold. It may propagate by causing PrPc to adopt its own infectious conformation by an unknown mechanism. Stud...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1996.0487
更新日期:1996-09-06 00:00:00
abstract::Polyglutamine (polyQ) amyloid fibrils are observed in disease tissue and have been implicated as toxic agents responsible for neurodegeneration in expanded CAG repeat diseases such as Huntington's disease. Despite intensive efforts, the mechanism of amyloid toxicity remains unknown. As a novel approach to probing poly...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2013.11.019
更新日期:2014-02-20 00:00:00