NMR structure of activated CheY.

Abstract:

:The CheY protein is the response regulator in bacterial chemotaxis. Phosphorylation of a conserved aspartyl residue induces structural changes that convert the protein from an inactive to an active state. The short half-life of the aspartyl-phosphate has precluded detailed structural analysis of the active protein. Persistent activation of Escherichia coli CheY was achieved by complexation with beryllofluoride (BeF(3)(-)) and the structure determined by NMR spectroscopy to a backbone r.m.s.d. of 0.58(+/-0.08) A. Formation of a hydrogen bond between the Thr87 OH group and an active site acceptor, presumably Asp57.BeF(3)(-), stabilizes a coupled rearrangement of highly conserved residues, Thr87 and Tyr106, along with displacement of beta4 and H4, to yield the active state. The coupled rearrangement may be a more general mechanism for activation of receiver domains.

journal_name

J Mol Biol

authors

Cho HS,Lee SY,Yan D,Pan X,Parkinson JS,Kustu S,Wemmer DE,Pelton JG

doi

10.1006/jmbi.2000.3595

keywords:

subject

Has Abstract

pub_date

2000-03-31 00:00:00

pages

543-51

issue

3

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(00)93595-2

journal_volume

297

pub_type

杂志文章
  • Nucleotide-Free sB-Raf is Preferentially Bound by Hsp90 and Cdc37 In Vitro.

    abstract::The molecular chaperone Hsp90 and its cofactor Cdc37 are required for the stability of protein kinases in the cellular environment. Upon pharmacological inhibition of Hsp90, the Hsp90-dependent kinases are degraded quickly by the proteasome. Clear physiological evidence for the formation of heterooligomeric complexes ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.09.002

    authors: Eckl JM,Daake M,Schwartz S,Richter K

    更新日期:2016-10-09 00:00:00

  • Protein structure comparison by alignment of distance matrices.

    abstract::With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. We have developed a novel algorithm (DALI) for optimal pairwise alignment of protein structures. The three-dimensional co-ordinates of each protein are used to calculate residu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1489

    authors: Holm L,Sander C

    更新日期:1993-09-05 00:00:00

  • Identification of novel alternative splicing events in the huntingtin gene and assessment of the functional consequences using structural protein homology modelling.

    abstract::Huntington's disease (HD) is an inherited progressive neurodegenerative disorder caused by a pathological CAG trinucleotide repeat expansion in the large multi-exon gene, huntingtin (HTT). Although multiple pathogenic mechanisms have been proposed for HD, there is increasing interest in the RNA processing of the HTT g...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.12.028

    authors: Hughes AC,Mort M,Elliston L,Thomas RM,Brooks SP,Dunnett SB,Jones L

    更新日期:2014-04-03 00:00:00

  • Crystal structure of an active form of human MMP-1.

    abstract::The extracellular matrix is a dynamic environment that constantly undergoes remodelling and degradation during vital physiological processes such as angiogenesis, wound healing, and development. Unbalanced extracellular matrix breakdown is associated with many diseases such as arthritis, cancer and fibrosis. Interstit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.06.079

    authors: Iyer S,Visse R,Nagase H,Acharya KR

    更新日期:2006-09-08 00:00:00

  • Translation elongation factor EF-Tu modulates filament formation of actin-like MreB protein in vitro.

    abstract::EF-Tu has been shown to interact with actin-like protein MreB and to affect its localization in Escherichia coli and in Bacillus subtilis cells. We have purified YFP-MreB in an active form, which forms filaments on glass slides in vitro and was active in dynamic light-scattering assays, polymerizing in milliseconds af...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.01.025

    authors: Defeu Soufo HJ,Reimold C,Breddermann H,Mannherz HG,Graumann PL

    更新日期:2015-04-24 00:00:00

  • Serpin acceleration of amyloid fibril formation: a role for accessory proteins.

    abstract::Protein aggregation underlies an increasing number of human diseases. Recent experiments have shown that the aggregation reaction is exquisitely specific involving particular interactions between non-native proteins. However, aggregation of certain proteins, for example beta-amyloid, in vivo leads to the recruitment o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.11.062

    authors: Powers GA,Pham CL,Pearce MC,Howlett GJ,Bottomley SP

    更新日期:2007-02-16 00:00:00

  • Evidence indicating proximity in the nucleosome between the histone H4 N termini and the globular domain of histone H1.

    abstract::Proteolysis of rat liver chromatin by the Arg-C peptidase, clostripain, is characterized by a progressive fragmentation of the N-terminal segments of the four core histones H2A, H2B, H3 and H4, until a well-defined limit digest is reached. This work addresses the case of histone H4. Two intermediate proteolytic sites ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1629

    authors: Banères JL,Essalouh L,Jariel-Encontre I,Mesnier D,Garrod S,Parello J

    更新日期:1994-10-14 00:00:00

  • Ligand-induced conformational changes via flexible linkers in the amino-terminal region of the inositol 1,4,5-trisphosphate receptor.

    abstract::Cytoplasmic Ca2+ signals are highly regulated by various ion transporters, including the inositol 1,4,5-trisphosphate (IP(3)) receptor (IP(3)R), which functions as a Ca2+ release channel on the endoplasmic reticulum membrane. Crystal structures of the two N-terminal regulatory regions from type 1 IP(3)R have been repo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.08.057

    authors: Chan J,Whitten AE,Jeffries CM,Bosanac I,Mal TK,Ito J,Porumb H,Michikawa T,Mikoshiba K,Trewhella J,Ikura M

    更新日期:2007-11-09 00:00:00

  • A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli.

    abstract::As enzymes evolve and diverge from common ancestor sequences, they often keep their overall reaction chemistry but specialize in the binding of different cognate ligands. This study borrows methods for the computational assessment of 2D similarity of small molecules from the field of chemoinformatics, to examine the e...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.01.061

    authors: Nobeli I,Spriggs RV,George RA,Thornton JM

    更新日期:2005-03-25 00:00:00

  • Refined structure of rat Clara cell 17 kDa protein at 3.0 A resolution.

    abstract::The rat Clara cell 17 kDa protein (previously referred to as the rat Clara cell 10 kDa protein) has been reported to inhibit phospholipase A2 and papain, and to also bind progesterone. It has been isolated from rat lung lavage fluid and crystallized in the space group P6(5)22. The structure has been determined to 3.0 ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)91006-b

    authors: Umland TC,Swaminathan S,Furey W,Singh G,Pletcher J,Sax M

    更新日期:1992-03-20 00:00:00

  • A new model for Schizosaccharomyces pombe telomere recognition: the telomeric single-stranded DNA-binding activity of Pot11-389.

    abstract::The protection of telomeres 1 (Pot1) proteins specifically recognize the single-stranded 3' end of the telomere, an activity essential for sustained cellular viability and proliferation. The current model for the telomeric single-stranded DNA (ssDNA) binding activity of Schizosaccharomyces pombe Pot1 is based on a 20 ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.06.002

    authors: Croy JE,Podell ER,Wuttke DS

    更新日期:2006-08-04 00:00:00

  • The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions.

    abstract::Crystal structures of two complexes between recombinant MS2 capsids and RNA operator fragments have been determined at 2.7 A resolution. The coat protein of the RNA bacteriophage MS2 is bifunctional; it forms the icosahedral virus shell to protect the viral nucleic acid and it acts as a translational repressor by bind...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1144

    authors: Valegârd K,Murray JB,Stonehouse NJ,van den Worm S,Stockley PG,Liljas L

    更新日期:1997-08-01 00:00:00

  • Role of a single amino acid in the evolution of glycans of invertebrates and vertebrates.

    abstract::Structures of glycoconjugate N-glycans and glycolipids of invertebrates show significant differences from those of vertebrates. These differences are due largely to the vertebrate beta1,4-galactosyltransferase-1 (beta4Gal-T1), which is found as a beta1,4-N-acetylgalactosaminyltransferase (beta4GalNAc-T1) in invertebra...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.10.034

    authors: Ramakrishnan B,Qasba PK

    更新日期:2007-01-19 00:00:00

  • Antifreeze protein from freeze-tolerant grass has a beta-roll fold with an irregularly structured ice-binding site.

    abstract::The grass Lolium perenne produces an ice-binding protein (LpIBP) that helps this perennial tolerate freezing by inhibiting the recrystallization of ice. Ice-binding proteins (IBPs) are also produced by freeze-avoiding organisms to halt the growth of ice and are better known as antifreeze proteins (AFPs). To examine th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.01.032

    authors: Middleton AJ,Marshall CB,Faucher F,Bar-Dolev M,Braslavsky I,Campbell RL,Walker VK,Davies PL

    更新日期:2012-03-09 00:00:00

  • Reconstituted and native iron-cores of bacterioferritin and ferritin.

    abstract::The structural and magnetic properties of the iron-cores of reconstituted horse spleen ferritin and Azotobacter vinelandii bacterioferritin have been investigated by high-resolution transmission electron microscopy, electron diffraction and Mossbauer spectroscopy. The structural properties of native horse spleen ferri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90290-7

    authors: Mann S,Williams JM,Treffry A,Harrison PM

    更新日期:1987-12-05 00:00:00

  • Analysis of the relationship between side-chain conformation and secondary structure in globular proteins.

    abstract::The relationship between the preferred side-chain dihedral angles and the secondary structure of a residue was examined. The structures of 61 proteins solved to a resolution of 2.0 A (1 A = 0.1 nm) or better were analysed using a relational database to store the information. The strongest feature observed was that the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90314-7

    authors: McGregor MJ,Islam SA,Sternberg MJ

    更新日期:1987-11-20 00:00:00

  • Structure-function defects of the TWINKLE linker region in progressive external ophthalmoplegia.

    abstract::TWINKLE is the helicase at the mitochondrial DNA (mtDNA) replication fork in mammalian cells. Mutations in the PEO1 gene, which encodes TWINKLE, cause autosomal dominant progressive external ophthalmoplegia (AdPEO), a disorder associated with deletions in mtDNA. Here, we characterized seven different AdPEO-causing mut...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.01.035

    authors: Korhonen JA,Pande V,Holmlund T,Farge G,Pham XH,Nilsson L,Falkenberg M

    更新日期:2008-03-28 00:00:00

  • Structure and function of the hairpin ribozyme.

    abstract::The hairpin ribozyme belongs to the family of small catalytic RNAs that cleave RNA substrates in a reversible reaction that generates 2',3'-cyclic phosphate and 5'-hydroxyl termini. The hairpin catalytic motif was discovered in the negative strand of the tobacco ringspot virus satellite RNA, where hairpin ribozyme-med...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1006/jmbi.2000.3560

    authors: Fedor MJ

    更新日期:2000-03-24 00:00:00

  • Architecture and flexibility of the yeast Ndc80 kinetochore complex.

    abstract::Kinetochores mediate microtubule-chromosome attachment and ensure accurate segregation of sister chromatids. The highly conserved Ndc80 kinetochore complex makes direct contacts with the microtubule and is essential for spindle checkpoint signaling. It contains a long coiled-coil region with globular domains at each e...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.08.077

    authors: Wang HW,Long S,Ciferri C,Westermann S,Drubin D,Barnes G,Nogales E

    更新日期:2008-11-21 00:00:00

  • Effect of organic co-solvents on the dimer/tetramer equilibrium of human haemoglobin.

    abstract::We have studied the effect of organic co-solvents (monohydric alcohols and formamide) on the dimer-tetramer equilibrium of human haemoglobin by measuring the dependence of oxygen affinity upon haemoglobin concentration over a 100-fold concentration range and analysing the data with a modified Monod-Wyman-Changeux mode...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90514-0

    authors: Cupane A,Vitrano E,Cordone L

    更新日期:1986-05-20 00:00:00

  • Elucidation of the active conformation of the APS-kinase domain of human PAPS synthetase 1.

    abstract::Bifunctional human PAPS synthetase (PAPSS) catalyzes, in a two-step process, the formation of the activated sulfate carrier 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The first reaction involves the formation of the 5'-adenosine phosphosulfate (APS) intermediate from ATP and inorganic sulfate. APS is then further p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.01.025

    authors: Sekulic N,Dietrich K,Paarmann I,Ort S,Konrad M,Lavie A

    更新日期:2007-03-23 00:00:00

  • Partitioning of plasmid R1. Ten direct repeats flanking the parA promoter constitute a centromere-like partition site parC, that expresses incompatibility.

    abstract::The parA partitioning system of plasmid R1 consists of three different components: the cis-acting centromere-like parC site, and the two trans-acting proteins ParM and ParR. These three components are contained within a region of 1.6 kb. The parC site is located upstream of the two genes, parM and parR, which are expr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(94)90058-2

    authors: Dam M,Gerdes K

    更新日期:1994-03-11 00:00:00

  • E. coli NusG inhibits backtracking and accelerates pause-free transcription by promoting forward translocation of RNA polymerase.

    abstract::NusG is an essential transcription factor in Escherichia coli that is capable of increasing the overall rate of transcription. Transcript elongation by RNA polymerase (RNAP) is frequently interrupted by pauses of varying durations, and NusG is known to decrease the occupancy of at least some paused states. However, it...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.03.051

    authors: Herbert KM,Zhou J,Mooney RA,Porta AL,Landick R,Block SM

    更新日期:2010-05-28 00:00:00

  • Recognition of herpes simplex viruses: toll-like receptors and beyond.

    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

    authors: Ma Y,He B

    更新日期:2014-03-20 00:00:00

  • The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement.

    abstract::We have used nuclear magnetic resonance (NMR) to obtain the structure of an RNA "kissing" hairpin complex formed between the HIV-2 TAR hairpin loop and a hairpin with a complementary loop sequence. Kissing hairpins are important in natural antisense reactions; their complex is a specific target for protein binding. Th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1021

    authors: Chang KY,Tinoco I Jr

    更新日期:1997-05-30 00:00:00

  • Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate.

    abstract::The folding/unfolding pathway of barnase has been studied extensively using the protein engineering method, which has provided indirect structural information for the transition state and the major folding intermediate. To further characterize the structural properties of the intermediate, we have simulated the therma...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1484

    authors: Li A,Daggett V

    更新日期:1998-01-30 00:00:00

  • Reconstitution and analysis of the multienzyme Escherichia coli RNA degradosome.

    abstract::The Escherichia coli RNA degradosome is a multienzyme assembly that functions in transcript turnover and maturation of structured RNA precursors. We have developed a procedure to reconstitute the RNA degradosome from recombinant components using modular coexpression vectors. The reconstituted assembly can be purified ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.07.059

    authors: Worrall JA,Górna M,Crump NT,Phillips LG,Tuck AC,Price AJ,Bavro VN,Luisi BF

    更新日期:2008-10-17 00:00:00

  • Characterization of human cytomegalovirus uracil DNA glycosylase (UL114) and its interaction with polymerase processivity factor (UL44).

    abstract::Here, we report the molecular characterization of the human cytomegalovirus uracil DNA glycosylase (UNG) UL114. Purified UL114 was shown to be a DNA glycosylase, which removes uracil from double-stranded and single-stranded DNA. However, kinetic analysis has shown that viral UNG removed uracil more slowly compared wit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.05.028

    authors: Ranneberg-Nilsen T,Dale HA,Luna L,Slettebakk R,Sundheim O,Rollag H,Bjørås M

    更新日期:2008-08-29 00:00:00

  • Single amino acid changes in the Bacillus thuringiensis var. israelensis delta-endotoxin affect the toxicity and expression of the protein.

    abstract::Site-directed mutagenesis has been used to change individual amino acids of the larvicidal 27,000 Mr delta-endotoxin of Bacillus thuringiensis var. israelensis. Basic and acidic residues have been systematically replaced by alanine, and the resulting mutant polypeptides analysed for cytolytic and larvicidal activity, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90283-5

    authors: Ward ES,Ellar DJ,Chilcott CN

    更新日期:1988-08-05 00:00:00

  • Probing dimerization and structural flexibility of mammalian lipoxygenases by small-angle X-ray scattering.

    abstract::Human lipoxygenases (LOXs) and their metabolites have a great impact on human homeostasis and are of interest for targeted drug design. This goal requires detailed knowledge of their structures and an understanding of structure-function relationship. At the moment, there are two complete crystal structures for mammali...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.04.035

    authors: Shang W,Ivanov I,Svergun DI,Borbulevych OY,Aleem AM,Stehling S,Jankun J,Kühn H,Skrzypczak-Jankun E

    更新日期:2011-06-17 00:00:00