scholarly journals Structure-Based Site-Directed Mutagenesis of the UDP-MurNAc-Pentapeptide-Binding Cavity of the FemX Alanyl Transferase from Weissella viridescens

2005 ◽  
Vol 187 (11) ◽  
pp. 3833-3838 ◽  
Author(s):  
Antoine P. Maillard ◽  
Sabrina Biarrotte-Sorin ◽  
Régis Villet ◽  
Stéphane Mesnage ◽  
Ahmed Bouhss ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Transferase Activity ◽  
Hydrogen Bond Network ◽  
Gram Positive Bacteria ◽  
Binding Cavity ◽  
Bond Network ◽  
Phosphate Groups

ABSTRACT Weissella viridescens FemX (FemXWv) belongs to the Fem family of nonribosomal peptidyl transferases that use aminoacyl-tRNA as the amino acid donor to synthesize the peptide cross-bridge found in the peptidoglycan of many species of pathogenic gram-positive bacteria. We have recently solved the crystal structure of FemXWv in complex with the peptidoglycan precursor UDP-MurNAc-pentapeptide and report here the site-directed mutagenesis of nine residues located in the binding cavity for this substrate. Two substitutions, Lys36Met and Arg211Met, depressed FemXWv transferase activity below detectable levels without affecting protein folding. Analogues of UDP-MurNAc-pentapeptide lacking the phosphate groups or the C-terminal d-alanyl residues were not substrates of the enzyme. These results indicate that Lys36 and Arg211 participate in a complex hydrogen bond network that connects the C-terminal d-Ala residues to the phosphate groups of UDP-MurNAc-pentapeptide and constrains the substrate in a conformation that is essential for transferase activity.

(NH4)[B3PO6(OH)3]·0.5H2O

2007 ◽  
Vol 63 (11) ◽  
pp. i185-i185 ◽  
Author(s):  
Wei Liu ◽  
Jingtai Zhao
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Ammonium Ions ◽  
One Dimensional ◽  
Bond Network ◽  
Solvothermal Conditions

The title compound, ammonium catena-[monoboro-monodihydrogendiborate-monohydrogenphosphate] hemihydrate, was obtained under solvothermal conditions using glycol as the solvent. The crystal structure is constructed of one-dimensional infinite borophosphate chains, which are interconnected by ammonium ions and water molecules via a complex hydrogen-bond network to form a three-dimensional structure. The water molecules of crystallization are disordered over inversion centres, and their H atoms were not located.

scholarly journals Conformational communication mediates the reset step in t6A biosynthesis

2019 ◽  
Vol 47 (12) ◽  
pp. 6551-6567 ◽  
Author(s):  
Amit Luthra ◽  
Naduni Paranagama ◽  
William Swinehart ◽  
Susan Bayooz ◽  
Phuc Phan ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Docking ◽  
Atpase Activity ◽  
Atp Hydrolysis ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Translational Fidelity ◽  
Substrate Analog ◽  
Binding Cavity ◽  
Saxs Analysis

Abstract The universally conserved N6-threonylcarbamoyladenosine (t6A) modification of tRNA is essential for translational fidelity. In bacteria, t6A biosynthesis starts with the TsaC/TsaC2-catalyzed synthesis of the intermediate threonylcarbamoyl adenylate (TC–AMP), followed by transfer of the threonylcarbamoyl (TC) moiety to adenine-37 of tRNA by the TC-transfer complex comprised of TsaB, TsaD and TsaE subunits and possessing an ATPase activity required for multi-turnover of the t6A cycle. We report a 2.5-Å crystal structure of the T. maritima TC-transfer complex (TmTsaB2D2E2) bound to Mg2+-ATP in the ATPase site, and substrate analog carboxy-AMP in the TC-transfer site. Site directed mutagenesis results show that residues in the conserved Switch I and Switch II motifs of TsaE mediate the ATP hydrolysis-driven reactivation/reset step of the t6A cycle. Further, SAXS analysis of the TmTsaB2D2-tRNA complex in solution reveals bound tRNA lodged in the TsaE binding cavity, confirming our previous biochemical data. Based on the crystal structure and molecular docking of TC–AMP and adenine-37 in the TC-transfer site, we propose a model for the mechanism of TC transfer by this universal biosynthetic system.

Hydrogen-bond network and pH sensitivity in transthyretin: Neutron crystal structure of human transthyretin

2012 ◽  
Vol 177 (2) ◽  
pp. 283-290 ◽  
Author(s):  
Takeshi Yokoyama ◽  
Mineyuki Mizuguchi ◽  
Yuko Nabeshima ◽  
Katsuhiro Kusaka ◽  
Taro Yamada ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Ph Sensitivity ◽  
Hydrogen Bond Network ◽  
Bond Network

L-2-Aminobutyric acid: two fully ordered polymorphs with Z′ = 4

2010 ◽  
Vol 66 (2) ◽  
pp. 253-259 ◽  
Author(s):  
Carl Henrik Görbitz
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Diffraction Data ◽  
Aminobutyric Acid ◽  
Side Chain ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Space Groups ◽  
Bond Network

The crystal structure of L-2-aminobutyric acid, an L-alanine analogue with an ethyl rather than a methyl side chain, has proved elusive owing to problems growing diffraction quality crystals. Good diffraction data have now been obtained for two polymorphs, in space groups P21 and I2, revealing surprisingly complex, yet fully ordered crystalline arrangements with Z′ = 4. The closely related structures are divided into hydrophilic and hydrophobic layers, the latter being the thinnest ever found for an amino acid (other than α-glycine). The hydrophobic layers furthermore contain conspicuous pseudo-centers-of-symmetry, leading to overall centrosymmetric intensity statistics. Uniquely, the four molecules in the asymmetric unit can be divided into two pairs that each forms an independent hydrogen-bond network.

The weakly coordinating perchlorate group in bis(N,N′-dimethylethylenediamine-κ2N,N′)bis(perchlorato-κO)copper(II) studied at 100, 250 and 400 K

2012 ◽  
Vol 68 (9) ◽  
pp. m251-m254 ◽  
Author(s):  
Silvia Schnitzler ◽  
Mihaela-Diana Şerb ◽  
Ulli Englert
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Title Compound ◽  
Two Dimensional ◽  
Hydrogen Bond Network ◽  
Distorted Octahedral ◽  
Jahn Teller ◽  
Mode Characteristic ◽  
Bond Network ◽  
Complex Forms

The crystal structure of the title compound, [Cu(ClO4)2(C4H12N2)2], (I), is reported at 100, 250 and 400 K. The CuIIcation in this complex is coordinated in a distorted octahedral mode characteristic of Jahn–Teller systems. The coordination of the perchlorate ligandsvialonger, and presumably weaker, axial Cu—O distances varies significantly as a function of temperature. One of the Cu—O distances increases between 100 and 250 K, and one of the Cu—O—Cl angles expands between 250 and 400 K. At all temperatures, the complex forms a two-dimensional N—H...O hydrogen-bond network in the (001) plane.

scholarly journals Crystal structure of a calcium(II)–pyrroloquinoline quinone (PQQ) complex outside a protein environment

2020 ◽  
Vol 76 (12) ◽  
pp. 1051-1056
Author(s):  
Henning Lumpe ◽  
Peter Mayer ◽  
Lena J. Daumann
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Crystal Structures ◽  
Pyrroloquinoline Quinone ◽  
Crystal Structure Analysis ◽  
Hydrogen Bond Network ◽  
Alcohol Dehydrogenases ◽  
Bond Network ◽  
Similarities And Differences ◽  
Protein Environment

Pyrroloquinoline quinone (PQQ) is an important cofactor of calcium- and lanthanide-dependent alcohol dehydrogenases, and has been known for over 30 years. Crystal structures of Ca–MDH enzymes (MDH is methanol dehydrogenase) have been known for some time; however, crystal structures of PQQ with biorelevant metal ions have been lacking in the literature for decades. We report here the first crystal structure analysis of a Ca–PQQ complex outside the protein environment, namely, poly[[undecaaquabis(μ-4,5-dioxo-4,5-dihydro-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylato)tricalcium(II)] dihydrate], {[Ca3(C14H3N2O8)2(H2O)11]·2H2O} n . The complex crystallized as Ca3PQQ2·13H2O with Ca2+ in three different positions and PQQ3−, including an extensive hydrogen-bond network. Similarities and differences to the recently reported structure with biorelevant europium (Eu2PQQ2) are discussed.

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