scholarly journals Functional assignment based on structural analysis: Crystal structure of the yggJ protein (HI0303) ofHaemophilus influenzae reveals an RNA methyltransferase with a deep trefoil knot

2003 ◽  
Vol 53 (2) ◽  
pp. 329-332 ◽  
Author(s):  
Farhad Forouhar ◽  
Jianwei Shen ◽  
Rong Xiao ◽  
Thomas B. Acton ◽  
Gaetano T. Montelione ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Functional Assignment ◽  
Trefoil Knot ◽  
Ofhaemophilus Influenzae

scholarly journals Structural basis for methyl-donor–dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD

2015 ◽  
Vol 112 (31) ◽  
pp. E4197-E4205 ◽  
Author(s):  
Takuhiro Ito ◽  
Isao Masuda ◽  
Ken-ichi Yoshida ◽  
Sakurako Goto-Ito ◽  
Shun-ichi Sekine ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Specific Binding ◽  
Structural Basis ◽  
Dependent Manner ◽  
Transfer Rnas ◽  
Methyl Donor ◽  
Trefoil Knot ◽  
Domains Of Life ◽  
Trna Methyltransferase

The deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life. In bacteria, TrmD catalyzes the N1-methylguanosine (m1G) modification at position 37 in transfer RNAs (tRNAs) with the 36GG37 sequence, using S-adenosyl-l-methionine (AdoMet) as the methyl donor. The m1G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome. Here we report the crystal structure of the TrmD homodimer in complex with a substrate tRNA and an AdoMet analog. Our structural analysis revealed the mechanism by which TrmD binds the substrate tRNA in an AdoMet-dependent manner. The trefoil-knot center, which is structurally conserved among SPOUT MTases, accommodates the adenosine moiety of AdoMet by loosening/retightening of the knot. The TrmD-specific regions surrounding the trefoil knot recognize the methionine moiety of AdoMet, and thereby establish the entire TrmD structure for global interactions with tRNA and sequential and specific accommodations of G37 and G36, resulting in the synthesis of m1G37-tRNA.

scholarly journals Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate

2015 ◽  
Vol 71 (2) ◽  
pp. 199-205 ◽  
Author(s):  
George T. Lountos ◽  
Scott Cherry ◽  
Joseph E. Tropea ◽  
David S. Waugh
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Phosphatase Activity ◽  
Small Molecule ◽  
Molecular Basis ◽  
Protein Tyrosine Phosphatases ◽  
Simple Method ◽  
Dual Specificity Phosphatase ◽  
Dual Specificity ◽  
Nitrophenyl Phosphate

4-Nitrophenyl phosphate (p-nitrophenyl phosphate, pNPP) is widely used as a small molecule phosphotyrosine-like substrate in activity assays for protein tyrosine phosphatases. It is a colorless substrate that upon hydrolysis is converted to a yellow 4-nitrophenolate ion that can be monitored by absorbance at 405 nm. Therefore, the pNPP assay has been widely adopted as a quick and simple method to assess phosphatase activity and is also commonly used in assays to screen for inhibitors. Here, the first crystal structure is presented of a dual-specificity phosphatase, human dual-specificity phosphatase 22 (DUSP22), in complex with pNPP. The structure illuminates the molecular basis for substrate binding and may also facilitate the structure-assisted development of DUSP22 inhibitors.

scholarly journals Multi-scale structural analysis of the A-site and oxygen deficient perovskite Sr11Mo4O23

2017 ◽  
Vol 46 (37) ◽  
pp. 12466-12473 ◽  
Author(s):  
Graham King ◽  
Maxim Avdeev ◽  
Ilyas Qasim ◽  
Qingi Zhou ◽  
Brendan J. Kennedy
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Multi Scale ◽  
Local Correlations ◽  
A Site

The crystal structure of Sr11Mo4O23 and the local correlations between the disordered sites are examined.

scholarly journals 1,1′,3,3′-Tetramesitylquinobis(imidazole)-2,2′-dithione

IUCrData ◽  
2019 ◽  
Vol 4 (9) ◽  
Author(s):  
Jayaraman Selvakumar ◽  
Kuppuswamy Arumugam
Keyword(s):  
Crystal Structure ◽  
Molecular Weight ◽  
Solid State ◽  
Structural Analysis ◽  
Hydrogen Bonds ◽  
Cell Volume ◽  
Title Compound ◽  
Unit Cell Volume ◽  
Density Peaks ◽  
Solvent Molecules

The solid-state structural analysis of the title compound [systematic name: 5,11-disulfanylidene-4,6,10,12-tetrakis(2,4,6-trimethylphenyl)-4,6,10,12-tetraazatricyclo[7.3.0.03,7]dodeca-1(9),3(7)-diene-2,8-dione], C44H44N4O2S2 [+solvent], reveals that the molecule crystallizes in a highly symmetric cubic space group so that one quarter of the molecule is crystallographically unique, the molecule lying on special positions (two mirror planes, two twofold axes and a center of inversion). The crystal structure exhibits large cavities of 193 Å3 accounting for 7.3% of the total unit-cell volume. These cavities contain residual density peaks but it was not possible to unambiguously identify the solvent therein. The contribution of the disordered solvent molecules to the scattering was removed using a solvent mask and is not included in the reported molecular weight. No classical hydrogen bonds are observed between the main molecules.

The synthesis, molecular and crystal structure of the 1:1 adduct of triphenyltin chloride with 2,3-diphenylthiazolidin-4-one

1995 ◽  
Vol 73 (1) ◽  
pp. 95-99 ◽  
Author(s):  
Frank E. Smith ◽  
Rosemary C. Hynes ◽  
John Tierney ◽  
Ying Z. Zhang ◽  
George Eng
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Oxygen Atom ◽  
Dutch Elm Disease ◽  
Monoclinic Space Group ◽  
Monodentate Ligand ◽  
X Ray ◽  
Trigonal Bipyramidal ◽  
Triphenyltin Chloride ◽  
Mössbauer Data

The title compound was synthesized as part of an effort to produce a more effective fungicide to combat Dutch Elm Disease (DED), which is caused by the fungus Ceratocystisulmi. A full X-ray structural analysis of the 1:1 adduct has been carried out and the results are reported along with the Mössbauer data for the compound. The crystals are monoclinic, space group P21/a with a = 19.240(3) Å, b = 9.1463(24) Å, c = 19.3512(24) Å, β = 118.874(8)°, V = 2982.0(10) Å3, z = 4, and Dcalc = 1.427 Mg m−3. The final discrepancy factors are RF = 0.056 and Rw = 0.058 for 1915 significant reflections. The QS and IS values in the Mössbauer spectrum of the complex are 3.08 mm s−1 and 1.28 mm s−1, respectively. The 2,3-diphenylthiazolidin-4-one behaves as a monodentate ligand and coordinates to the tin through the oxygen atom. The complex exhibits a trigonal bipyramidal configuration with the three phenyl groups in equatorial positions and the chloride and ligand oxygen occupying the apical sites. Keywords: triorganotin, fungicide, Dutch Elm Disease, thiazolidin-4-one.

Cyano-Bridged Bimetallic Complexes of Copper(II) with Nitroprusside. Crystal Structure of [Cu(H2NCH2CH(NH2)CH3)2Fe(CN)5NO] . H2O

2000 ◽  
Vol 53 (3) ◽  
pp. 225 ◽  
Author(s):  
Zdenek Smékal ◽  
Zdenek Trávnícek ◽  
Jaromír Marek ◽  
Milan Nádvornik
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Magnetic Measurements ◽  
X Ray ◽  
Cyanide Group ◽  
Cyanide Ligand ◽  
Binuclear Structure ◽  
Tetragonal Pyramidal ◽  
Cyanide Ligands ◽  
Diamine Ligands

Five new complexes of compositions [Cu(1,2-pn)2Fe(CN)5NO]·H2O (1,2-pn = propane-1,2-diamine) and [Cu(L)Fe(CN)5NO]·xH2O (L = tmen (N,N,N′,N′-tetramethylethane-1,2-diamine), x = 0.5; L = trimeen (N,N,N′-trimethylethane-1,2-diamine), x = 1; L = dien (N-(2-aminoethyl)ethane-1,2-diamine), x = 0; L = medpt (N-(3-aminopropyl)-N-methylpropane-1,3-diamine), x = 2) have been isolated from the reaction mixture of Cu(ClO4)2·6H2O (or CuCl2·2H2O), the amine and Na2 [Fe(CN)5NO]·2H2O in water. The complexes have been characterized by infrared and ultraviolet–visible spectroscopies, and magnetic measurements. Single-crystal X-ray structural analysis revealed that the [Cu(1,2-pn)2Fe(CN)5NO]·H2O complex assumes a cyanide-bridged binuclear structure in which iron(II) is six-coordinated by five cyanide ligands and one nitrosyl group (the nitrosyl group lies cis to the bridging cyanide group), while copper(II) is five-coordinated by two propane-1,2-diamine ligands and a bridging cyanide ligand in a distorted tetragonal pyramidal arrangement.

scholarly journals Unusual formation of (E)-11-(aminomethylene)-8,9,10,11-tetrahydropyrido[2′,3′:4,5]pyrimido[1,2-a]azepin-5(7H)-one and its crystal structure

2017 ◽  
Vol 73 (10) ◽  
pp. 1497-1500
Author(s):  
Khamid U. Khodjaniyazov ◽  
Utkir S. Makhmudov ◽  
Kambarali K. Turgunov ◽  
Burkhon Z. Elmuradov
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Aqueous Ammonia ◽  
Boat Conformation ◽  
X Ray ◽  
First Time ◽  
Twist Boat ◽  
Unusual Formation

Selective C-formylation of 8,9,10,11-tetrahydropyrido[2′,3′:4,5]pyrimido[1,2-a]-azepin-5(7H)-one has been studied for the first time. It was revealed that formylation proceeds by the formation of an intermediate salt, which due to the re-amination process on treatment with aqueous ammonia transformed into the corresponding (E)-11-(aminomethylene)-8,9,10,11-tetrahydropyrido[2′,3′:4,5]-pyrimido[1,2-a]azepin-5(7H)-one, C13H14N4O, as anE-isomer. Formylation was carried out by Vilsmeier–Haack reagent and the structure of the synthesized compound was confirmed by X-ray structural analysis, spectroscopic and LC–MS methods. In the molecule, the seven-membered pentamethylene ring adopts a twist-boat conformation.

scholarly journals Structural analysis of point mutations at theVaccinia virusA20/D4 interface

2016 ◽  
Vol 72 (9) ◽  
pp. 687-691 ◽  
Author(s):  
Céline Contesto-Richefeu ◽  
Nicolas Tarbouriech ◽  
Xavier Brazzolotto ◽  
Wim P. Burmeister ◽  
Christophe N. Peyrefitte ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acids ◽  
Structural Analysis ◽  
Complex Formation ◽  
Dna Polymerase ◽  
Point Mutations ◽  
Conformational Space ◽  
Uracil Dna Glycosylase ◽  
Dimerization Interface ◽  
Solvation Parameters

TheVaccinia viruspolymerase holoenzyme is composed of three subunits: E9, the catalytic DNA polymerase subunit; D4, a uracil-DNA glycosylase; and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase cofactor, the function of which is essential for processive DNA synthesis. The recent crystal structure of D4 bound to the first 50 amino acids of A20 (D4/A201–50) revealed the importance of three residues, forming a cation–π interaction at the dimerization interface, for complex formation. These are Arg167 and Pro173 of D4 and Trp43 of A20. Here, the crystal structures of the three mutants D4-R167A/A201–50, D4-P173G/A201–50and D4/A201–50-W43A are presented. The D4/A20 interface of the three structures has been analysed for atomic solvation parameters and cation–π interactions. This study confirms previous biochemical data and also points out the importance for stability of the restrained conformational space of Pro173. Moreover, these new structures will be useful for the design and rational improvement of known molecules targeting the D4/A20 interface.

Crystal structure of (Ph4P)[Hg(SPh)2Br]: Synthesis, characterization and structural analysis

2005 ◽  
Vol 35 (8) ◽  
pp. 589-594 ◽  
Author(s):  
Basem F. Ali
Keyword(s):  
Crystal Structure ◽  
Structural Analysis

Molecular and crystal structure of 1,4-diacethoxy naphthalene: Structural analysis of methyl substituted 1,4-diacethoxynaphthalenes

1989 ◽  
Vol 19 (2) ◽  
pp. 307-316
Author(s):  
Jos� Gonzalo Rodr�guez ◽  
Alfonso Pablo ◽  
Julian Lopez Lerma ◽  
Aurea Perales
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Molecular And Crystal Structure
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