当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Crystal structures of the complexes between vancomycin and cell-wall precursor analogs.

Crystal structures of the complexes between vancomycin and cell-wall precursor analogs.

Abstract：

:The crystal structures of three vancomycin complexes with two vancomycin-sensitive cell-wall precursor analogs (diacetyl-Lys-D-Ala-D-Ala and acetyl-D-Ala-D-Ala) and a vancomycin-resistant cell-wall precursor analog (diacetyl-Lys-D-Ala-D-lactate) were determined at atomic resolutions of 1.80 A, 1.07 A, and 0.93 A, respectively. These structures not only reconfirm the "back-to-back" dimerization of vancomycin monomers and the ligand-binding scheme proposed by previous experiments but also show important structural features of strategies for the generation of new glycopeptide antibiotics. These structural features involve a water-mediated antibiotic-ligand interaction and supramolecular structures such as "side-by-side" arranged dimer-to-dimer structures, in addition to ligand-mediated and "face-to-face" arranged dimer-to-dimer structures. In the diacetyl-Lys-D-Ala-D-lactate complex, the interatomic O...O distance between the carbonyl oxygen of the fourth residue of the antibiotic backbone and the ester oxygen of the D-lactate moiety of the ligand is clearly longer than the corresponding N-H...O hydrogen-bonding distance observed in the two other complexes due to electrostatic repulsion. In addition, two neighboring hydrogen bonds are concomitantly lengthened. These observations provide, at least in part, a molecular basis for the reduced antibacterial activity of vancomycin toward vancomycin-resistant bacteria with cell-wall precursors terminating in -D-Ala-D-lactate.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Nitanai Y,Kikuchi T,Kakoi K,Hanamaki S,Fujisawa I,Aoki K

doi

10.1016/j.jmb.2008.10.026

subject

Has Abstract

pub_date

2009-02-06 00:00:00

pages

1422-32

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(08)01302-8

journal_volume

385

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Determination of the pK(a) of the four Zn2+-coordinating residues of the distal finger motif of the HIV-1 nucleocapsid protein: consequences on the binding of Zn2+.

    abstract：:The nucleocapsid protein NCp7 of human immunodeficiency virus type 1 is characterized by two highly conserved CCHC motifs that bind Zn2+ strongly. To elucidate the striking pH-dependence of the apparent Zn2+-binding constants of these motifs further, we investigated, using 1H NMR, potentiometry and fluorescence spectr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4770

    authors： Bombarda E,Morellet N,Cherradi H,Spiess B,Bouaziz S,Grell E,Roques BP,Mély Y

    更新日期：2001-07-13 00:00:00

  • NMR structures of two variants of bovine pancreatic trypsin inhibitor (BPTI) reveal unexpected influence of mutations on protein structure and stability.

    abstract：:Here we determined NMR solution structures of two mutants of bovine pancreatic trypsin inhibitor (BPTI) to reveal structural reasons of their decreased thermodynamic stability. A point mutation, A16V, in the solvent-exposed loop destabilizes the protein by 20 degrees C, in contrast to marginal destabilization observed...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00620-4

    authors： Cierpicki T,Otlewski J

    更新日期：2002-08-23 00:00:00

  • Islet amyloid polypeptide forms rigid lipid-protein amyloid fibrils on supported phospholipid bilayers.

    abstract：:Islet amyloid polypeptide (IAPP) forms fibrillar amyloid deposits in the pancreatic islets of Langerhans of patients with type 2 diabetes mellitus, and its misfolding and aggregation are thought to contribute to beta-cell death. Increasing evidence suggests that IAPP fibrillization is strongly influenced by lipid memb...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.11.077

    authors： Domanov YA,Kinnunen PK

    更新日期：2008-02-08 00:00:00

  • Identification and molecular analysis of oxyR-regulated promoters important for the bacterial adaptation to oxidative stress.

    abstract：:The oxyR-encoded regulatory protein, OxyR, acts to induce the synthesis of a family of hydrogen peroxide-inducible proteins in Salmonella typhimurium and Escherichia coli. To further define the mechanism by which oxyR regulates the production of these proteins, we identified, mapped, and characterized oxyR-regulated p...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90104-6

    authors： Tartaglia LA,Storz G,Ames BN

    更新日期：1989-12-20 00:00:00

  • DNA topology-mediated regulation of transcription initiation from the tandem promoters of the ilvGMEDA operon of Escherichia coli.

    abstract：:It is becoming increasingly clear that the intrinsic and protein-induced topological properties of the DNA helix influence transcriptional efficiency. In this report we describe the properties of two upstream activating regions that influence transcription from the non-overlapping tandem promoters of the ilvGMEDA oper...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90460-2

    authors： Pagel JM,Winkelman JW,Adams CW,Hatfield GW

    更新日期：1992-04-20 00:00:00

  • Divergence in macromolecular assembly: X-ray crystallographic structure analysis of lumazine synthase from Brucella abortus.

    abstract：:We have determined the three-dimensional structure of 6, 7-dimethyl-8-ribityllumazine synthase (lumazine synthase) from Brucella abortus, the infectious organism of the disease brucellosis in animals. This enzyme catalyses the formation of 6, 7-dimethyl-8-ribityllumazine, the penultimate product in the synthesis of ri...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3640

    authors： Braden BC,Velikovsky CA,Cauerhff AA,Polikarpov I,Goldbaum FA

    更新日期：2000-04-14 00:00:00

  • Transition of chromatin from the "10 nm" lower order structure, to the "30 nm" higher order structure as followed by small angle X-ray scattering.

    abstract：:Chromatin oligomers undergo a conformational change from a "10 nm" lower order structure at low concentration of salt to a "30 nm" higher order structure, with increasing NaCl or MgCl2 concentration. We have extended our previously reported hydrodynamic and light-scattering measurements of the folding of well-defined ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90353-6

    authors： Greulich KO,Wachtel E,Ausio J,Seger D,Eisenberg H

    更新日期：1987-02-20 00:00:00

  • Genomic analysis of sequence variation in tandemly repeated DNA. Evidence for localized homogeneous sequence domains within arrays of alpha-satellite DNA.

    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

    authors： Warburton PE,Willard HF

    更新日期：1990-11-05 00:00:00

  • Ring closure probabilities for DNA fragments by Monte Carlo simulation.

    abstract：:The rate of ligation of DNA molecules into circular forms depends on the ring closure probability, commonly called the j-factor, which is a sensitive measure of the extent to which thermal fluctuations contribute to bending and twisting of DNA molecules in solution. We present a theoretical treatment of the cyclizatio...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90381-5

    authors： Levene SD,Crothers DM

    更新日期：1986-05-05 00:00:00

  • Cold-adaptation in sea-water-borne signal proteins: sequence and NMR structure of the pheromone En-6 from the Antarctic ciliate Euplotes nobilii.

    abstract：:Ciliates of Euplotes species constitutively secrete pleiotropic protein pheromones, which are capable to function as prototypic autocrine growth factors as well as paracrine inducers of mating processes. This paper reports the amino acid sequence and the NMR structure of the pheromone En-6 isolated from the antarctic ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.06.046

    authors： Pedrini B,Placzek WJ,Koculi E,Alimenti C,LaTerza A,Luporini P,Wüthrich K

    更新日期：2007-09-14 00:00:00

  • Brujita Integrase: A Simple, Arm-Less, Directionless, and Promiscuous Tyrosine Integrase System.

    abstract：:Mycobacteriophage Brujita is an unusual temperate phage in which establishment of superinfection immunity is dependent on chromosomal integration. Integration is mediated by a non-canonical tyrosine integrase (Int) lacking an N-terminal domain typically associated with binding to arm-type sites within the phage attach...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.04.023

    authors： Lunt BL,Hatfull GF

    更新日期：2016-06-05 00:00:00

  • DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site.

    abstract：:Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleot...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.10.036

    authors： Kearney BM,Johnson CW,Roberts DM,Swartz P,Mattos C

    更新日期：2014-02-06 00:00:00

  • Mitochondrial DNA Purifying Selection in Mammals and Invertebrates.

    abstract：:Numerous mitochondrial quality control mechanisms exist within cells, but none have been shown to effectively assess and control the quality of mitochondrial DNA (mtDNA). One reason such mechanisms have yet to be elucidated is that they do not appear to be particularly active in most somatic cells, where many studies ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2018.10.019

    authors： Palozzi JM,Jeedigunta SP,Hurd TR

    更新日期：2018-12-07 00:00:00

  • Characterization of hnRNP K protein-RNA interactions.

    abstract：:The heterogeneous nuclear ribonucleoprotein K protein is an RNA-binding protein found in several subcellular compartments where it is thought to be involved in signaling multiple processes that compose gene expression. K protein contains three K homology (KH) domains that mediate RNA-binding. We used a serial analysis...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.07.099

    authors： Klimek-Tomczak K,Wyrwicz LS,Jain S,Bomsztyk K,Ostrowski J

    更新日期：2004-09-24 00:00:00

  • Non-receptor tyrosine kinases c-Abl and Arg regulate the activity of C/EBPbeta.

    abstract：:The CCAAT/enhancer-binding protein beta (C/EBPbeta) is a critical transcription factor that regulates gene expression during numerous biological processes, including differentiation, metabolism, homeostasis, proliferation, tumorigenesis, inflammation, and apoptosis. In this study, interactions between C/EBPbeta and ei...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.06.055

    authors： Li X,Liu X,Wang G,Zhu X,Qu X,Li X,Yang Y,Peng L,Li C,Li P,Huang W,Ma Q,Cao C

    更新日期：2009-08-28 00:00:00

  • Crystallization and preliminary X-ray diffraction study of the ligand-binding domain of the bacterial chemotaxis-mediating aspartate receptor of Salmonella typhimurium.

    abstract：:The periplasmic domain of the aspartate chemotaxis receptor from Salmonella typhimurium has been crystallized in the presence and absence of bound aspartate. Both crystal forms were grown by precipitation with lithium sulfate and diffract to 1.8 A resolution. The aspartate receptor structure is believed to be prototyp...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)80198-4

    authors： Jancarik J,Scott WG,Milligan DL,Koshland DE Jr,Kim SH

    更新日期：1991-09-05 00:00:00

  • Conformational changes in the multidrug transporter EmrE associated with substrate binding.

    abstract：:EmrE is a bacterial multidrug transporter of the small multidrug resistance family, which extrudes large hydrophobic cations such as tetraphenylphosphonium (TPP(+)) out of the cell by a proton antiport mechanism. Binding measurements were performed on purified EmrE solubilized in dodecylmaltoside to determine the stoi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00895-7

    authors： Tate CG,Ubarretxena-Belandia I,Baldwin JM

    更新日期：2003-09-05 00:00:00

  • Location of high and low affinity fatty acid binding sites on human serum albumin revealed by NMR drug-competition analysis.

    abstract：:Human serum albumin (HSA) is an abundant plasma protein that transports a wide variety of drugs and endogenous compounds. The complex binding capacity of HSA has made it a challenging system to study in detail but in order to develop our understanding of the interactions between ligands for HSA, the locations and rela...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.06.028

    authors： Simard JR,Zunszain PA,Hamilton JA,Curry S

    更新日期：2006-08-11 00:00:00

  • Structurally constrained residues outside the binding motif are essential in the interaction of 14-3-3 and phosphorylated partner.

    abstract：:14-3-3 proteins participate in many key cellular processes after binding to disordered phospho-partners. Usually, the phosphorylated state is an essential target for the binding. Here, we show for the first time residues other than those in the 14-3-3 binding motif that are essential for the binding between 14-3-3 and...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.12.043

    authors： Uhart M,Iglesias AA,Bustos DM

    更新日期：2011-03-04 00:00:00

  • Mutations in beta-myosin S2 that cause familial hypertrophic cardiomyopathy (FHC) abolish the interaction with the regulatory domain of myosin-binding protein-C.

    abstract：:The myosin filaments of striated muscle contain a family of enigmatic myosin-binding proteins (MyBP), MyBP-C and MyBP-H. These modular proteins of the intracellular immunoglobulin superfamily contain unique domains near their N termini. The N-terminal domain of cardiac MyBP-C, the MyBP-C motif, contains additional pho...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2522

    authors： Gruen M,Gautel M

    更新日期：1999-02-26 00:00:00

  • Impact of the terminal bulges of HIV-1 cTAR DNA on its stability and the destabilizing activity of the nucleocapsid protein NCp7.

    abstract：:Reverse transcription of HIV-1 genomic RNA to double-stranded DNA by reverse transcriptase (RT) is a critical step in HIV-1 replication. This process relies on two viral proteins, the RT enzyme and nucleocapsid protein NCp7 that has well documented nucleic acid chaperone properties. At the beginning of the linear DNA ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00244-4

    authors： Beltz H,Azoulay J,Bernacchi S,Clamme JP,Ficheux D,Roques B,Darlix JL,Mély Y

    更新日期：2003-04-18 00:00:00

  • Co-optimization of ribozyme substrate stacking and L-arginine binding.

    abstract：:A model of the Tetrahymena catalytic site predicts that nucleotide 262 (nt262) caps an RNA pocket in which nucleoside substrates and arginine-like competitive inhibitors reside. Here we show that substituted RNAs behave as if nt262 stacks on nucleoside substrates, supporting the model. The more frequent an nt262 is in...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90095-2

    authors： Yarus M,Majerfeld I

    更新日期：1992-06-20 00:00:00

  • Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase.

    abstract：:The structure of the Escherichia coli Dam DNA-(adenine-N6)-methyltransferase in complex with cognate DNA was determined at 1.89 A resolution in the presence of S-adenosyl-L-homocysteine. DNA recognition and the dynamics of base-flipping were studied by site-directed mutagenesis, DNA methylation kinetics and fluorescen...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.02.028

    authors： Horton JR,Liebert K,Bekes M,Jeltsch A,Cheng X

    更新日期：2006-04-28 00:00:00

  • Archaeal N-terminal protein maturation commonly involves N-terminal acetylation: a large-scale proteomics survey.

    abstract：:We present the first large-scale survey of N-terminal protein maturation in archaea based on 873 proteomically identified N-terminal peptides from the two haloarchaea Halobacterium salinarum and Natronomonas pharaonis. The observed protein maturation pattern can be attributed to the combined action of methionine amino...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.07.086

    authors： Falb M,Aivaliotis M,Garcia-Rizo C,Bisle B,Tebbe A,Klein C,Konstantinidis K,Siedler F,Pfeiffer F,Oesterhelt D

    更新日期：2006-10-06 00:00:00

  • A novel allosteric mechanism in haemoglobin. Structure of bovine deoxyhaemoglobin, absence of specific chloride-binding sites and origin of the chloride-linked Bohr effect in bovine and human haemoglobin.

    abstract：:The structure of bovine deoxyhaemoglobin has been determined at 2.2 A resolution and refined to an R-factor of 0.193 for all 32,583 reflections, and a free R-factor of 0.249 for 1527 reflections excluded from the refinement. The structure shows no significant differences between the alpha-carbon positions of bovine an...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1530

    authors： Perutz MF,Fermi G,Poyart C,Pagnier J,Kister J

    更新日期：1993-10-05 00:00:00

  • Calcium binding sites in tomato bushy stunt virus visualized by Laue crystallography.

    abstract：:We have collected Laue diffraction data from crystals of tomato bushy stunt virus using the full white X-ray spectrum from the wiggler magnet of the Synchrotron Radiation Source at Daresbury, U.K. A single 24 second exposure of a crystal soaked in EDTA yielded a data set that was 90% complete between 6 and 3.5 A resol...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(90)90278-T

    authors： Campbell JW,Clifton IJ,Greenhough TJ,Hajdu J,Harrison SC,Liddington RC,Shrive AK

    更新日期：1990-08-05 00:00:00

  • An additional dimer linkage structure in Moloney murine leukemia virus RNA.

    abstract：:We have identified an additional dimerization linkage structure in the genome of Moloney murine leukemia virus (MoMLV). Retroviral genomes have long been known to be linked at their 5' ends to form dimers. In MoMLV, a hairpin loop functioning as a dimer linkage structure (DLS) has previously been identified at nucleot...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2984

    authors： Oroudjev EM,Kang PC,Kohlstaedt LA

    更新日期：1999-08-20 00:00:00

  • Functional model of subcomponent C1 of human complement.

    abstract：:The domain organization of the zymogen subunits of the first component of human complement C1s, C1r2 and the complex C1s-C1r2-C1s was studied by electron microscopy. In the absence of Ca2+, monomeric C1s was visualized as a dumb-bell-shaped molecule consisting of two globular domains (center-to-center distance 11 nm) ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90325-6

    authors： Weiss V,Fauser C,Engel J

    更新日期：1986-06-05 00:00:00

  • The complete nucleotide sequence of a plant root-inducing (Ri) plasmid indicates its chimeric structure and evolutionary relationship between tumor-inducing (Ti) and symbiotic (Sym) plasmids in Rhizobiaceae.

    abstract：:The Ri (root-inducing) plasmid in Agrobacterium rhizogenes and Ti (tumor-inducing) plasmid in Agrobacterium tumefaciens have provided the fundamental basis for the construction of plant vectors and transgenic plants. Recently, the determination of the first complete nucleotide sequence of the Ti plasmid (pTi-SAKURA) h...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4488

    authors： Moriguchi K,Maeda Y,Satou M,Hardayani NS,Kataoka M,Tanaka N,Yoshida K

    更新日期：2001-03-30 00:00:00

  • Crystal structure at 1.95 A resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition.

    abstract：:The anti-breast tumour antibody SM3 has a high selectivity in reacting specifically with carcinoma-associated mucin. SM3 recognises the core repeating motif (Pro-Asp-Thr-Arg-Pro) of aberrantly glycosylated epithelial mucin MUC1, and has potential as a therapeutic and diagnostic tool. Here we report the crystal structu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2209

    authors： Dokurno P,Bates PA,Band HA,Stewart LM,Lally JM,Burchell JM,Taylor-Papadimitriou J,Snary D,Sternberg MJ,Freemont PS

    更新日期：1998-12-04 00:00:00