scholarly journals Crystal structure of glycosyltrehalose synthase fromSulfolobus shibataeDSM5389

2018 ◽  
Vol 74 (11) ◽  
pp. 741-746
Author(s):  
Nobuo Okazaki ◽  
Michael Blaber ◽  
Ryota Kuroki ◽  
Taro Tamada
Keyword(s):  
Crystal Structure ◽  
Amino Acids ◽  
Catalytic Mechanism ◽  
Catalytic Domain ◽  
Structural Basis ◽  
Hyperthermophilic Archaeon ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sulfolobus Shibatae ◽  
Glucosidic Bond

Glycosyltrehalose synthase (GTSase) converts the glucosidic bond between the last two glucose residues of amylose from an α-1,4 bond to an α-1,1 bond, generating a nonreducing glycosyl trehaloside, in the first step of the biosynthesis of trehalose. To better understand the structural basis of the catalytic mechanism, the crystal structure of GTSase from the hyperthermophilic archaeonSulfolobus shibataeDSM5389 (5389-GTSase) has been determined to 2.4 Å resolution by X-ray crystallography. The structure of 5389-GTSase can be divided into five domains. The central domain contains the (β/α)8-barrel fold that is conserved as the catalytic domain in the α-amylase family. Three invariant catalytic carboxylic amino acids in the α-amylase family are also found in GTSase at positions Asp241, Glu269 and Asp460 in the catalytic domain. The shape of the catalytic cavity and the pocket size at the bottom of the cavity correspond to the intramolecular transglycosylation mechanism proposed from previous enzymatic studies.

scholarly journals X-Ray Crystal Structure of the Multidomain Endoglucanase Cel9G from Clostridium cellulolyticum Complexed with Natural and Synthetic Cello-Oligosaccharides

2003 ◽  
Vol 185 (14) ◽  
pp. 4127-4135 ◽  
Author(s):  
David Mandelman ◽  
Anne Belaich ◽  
J. P. Belaich ◽  
Nushin Aghajari ◽  
Hugues Driguez ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Domain ◽  
Cellulose Degradation ◽  
Cellulase Activity ◽  
Structural Basis ◽  
Crystalline Cellulose ◽  
X Ray ◽  
Clostridium Cellulolyticum ◽  
Active Site Cleft ◽  
Cellulose Binding

ABSTRACT Complete cellulose degradation is the first step in the use of biomass as a source of renewable energy. To this end, the engineering of novel cellulase activity, the activity responsible for the hydrolysis of the β-1,4-glycosidic bonds in cellulose, is a topic of great interest. The high-resolution X-ray crystal structure of a multidomain endoglucanase from Clostridium cellulolyticum has been determined at a 1.6-Å resolution. The endoglucanase, Cel9G, is comprised of a family 9 catalytic domain attached to a family IIIc cellulose-binding domain. The two domains together form a flat platform onto which crystalline cellulose is suggested to bind and be fed into the active-site cleft for endolytic hydrolysis. To further dissect the structural basis of cellulose binding and hydrolysis, the structures of Cel9G in the presence of cellobiose, cellotriose, and a DP-10 thio-oligosaccharide inhibitor were resolved at resolutions of 1.7, 1.8, and 1.9 Å, respectively.

scholarly journals Structural basis of Naa20 activity towards a canonical NatB substrate

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Dominik Layer ◽  
Jürgen Kopp ◽  
Miriam Fontanillo ◽  
Maja Köhn ◽  
Karine Lapouge ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Drug Development ◽  
Catalytic Mechanism ◽  
Peptide Binding ◽  
Competitive Inhibitor ◽  
Structural Basis ◽  
Substrate Affinity ◽  
Protein Homeostasis ◽  
Auxiliary Subunit

AbstractN-terminal acetylation is one of the most common protein modifications in eukaryotes and is carried out by N-terminal acetyltransferases (NATs). It plays important roles in protein homeostasis, localization, and interactions and is linked to various human diseases. NatB, one of the major co-translationally active NATs, is composed of the catalytic subunit Naa20 and the auxiliary subunit Naa25, and acetylates about 20% of the proteome. Here we show that NatB substrate specificity and catalytic mechanism are conserved among eukaryotes, and that Naa20 alone is able to acetylate NatB substrates in vitro. We show that Naa25 increases the Naa20 substrate affinity, and identify residues important for peptide binding and acetylation activity. We present the first Naa20 crystal structure in complex with the competitive inhibitor CoA-Ac-MDEL. Our findings demonstrate how Naa20 binds its substrates in the absence of Naa25 and support prospective endeavors to derive specific NAT inhibitors for drug development.

Verfeinerung der Kristallstruktur von Tripalladium-di-tetrathiophospliat Pd3(PS4)2 Refinement of the Crystal Structure of Tripalladium-di-tetrathiophosphate Pda3(PS4)2

1983 ◽  
Vol 38 (4) ◽  
pp. 426-427 ◽  
Author(s):  
Arndt Simon ◽  
Karl Peters ◽  
Harry Hahn
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Title Compound ◽  
Type Structure ◽  
Tetrahedral Symmetry ◽  
X Ray ◽  
X Ray Crystallography ◽  
Planar Environment

Abstract The structure of the title compound has been determined by X-ray crystallography. The title compound is synthesized from the elements at 600 °C. Its crystal structure, derived from powder data [3] is refined by single crystal diffractometer data. The structure is trigonal (P3̅ml, α = 684.1(1), c = 724.4(1) pm); Pd2+ cations and PS43- anions form a network with an anti-Claudetite (AS2O3) type structure. The PS4 units are distinctly distorted from ideal tetrahedral symmetry. The Pd atoms have a planar environment of 4 S atoms.

Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase

2010 ◽  
Vol 43 (5) ◽  
pp. 1113-1120 ◽  
Author(s):  
Esko Oksanen ◽  
François Dauvergne ◽  
Adrian Goldman ◽  
Monika Budayova-Spano
Keyword(s):  
Data Collection ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Catalytic Mechanism ◽  
Inorganic Pyrophosphatase ◽  
Neutron Diffraction Data ◽  
Cooling Device ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography

H atoms play a central role in enzymatic mechanisms, but H-atom positions cannot generally be determined by X-ray crystallography. Neutron crystallography, on the other hand, can be used to determine H-atom positions but it is experimentally very challenging. Yeast inorganic pyrophosphatase (PPase) is an essential enzyme that has been studied extensively by X-ray crystallography, yet the details of the catalytic mechanism remain incompletely understood. The temperature instability of PPase crystals has in the past prevented the collection of a neutron diffraction data set. This paper reports how the crystal growth has been optimized in temperature-controlled conditions. To stabilize the crystals during neutron data collection a Peltier cooling device that minimizes the temperature gradient along the capillary has been developed. This device allowed the collection of a full neutron diffraction data set.

The first crystal structure of the peptidase domain of the U32 peptidase family

2015 ◽  
Vol 71 (12) ◽  
pp. 2505-2512 ◽  
Author(s):  
Magdalena Schacherl ◽  
Angelika A. M. Montada ◽  
Elena Brunstein ◽  
Ulrich Baumann
Keyword(s):  
Crystal Structure ◽  
Catalytic Mechanism ◽  
Quaternary Structure ◽  
Catalytic Domain ◽  
Three Dimensional ◽  
Zinc Ion ◽  
Crystal Structure Analysis ◽  
Dimensional Structure ◽  
Sequence Motifs ◽  
Conserved Sequence

The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins fromHelicobacterandSalmonella. The first crystal structure analysis of a U32 catalytic domain fromMethanopyrus kandleri(genemk0906) reveals a modified (βα)8TIM-barrel fold with some unique features. The connecting segment between strands β7 and β8 is extended and helix α7 is located on top of the C-terminal end of the barrel body. The protein exhibits a dimeric quaternary structure in which a zinc ion is symmetrically bound by histidine and cysteine side chains from both monomers. These residues reside in conserved sequence motifs. No typical proteolytic motifs are discernible in the three-dimensional structure, and biochemical assays failed to demonstrate proteolytic activity. A tunnel in which an acetate ion is bound is located in the C-terminal part of the β-barrel. Two hydrophobic grooves lead to a tunnel at the C-terminal end of the barrel in which an acetate ion is bound. One of the grooves binds to aStrep-Tag II of another dimer in the crystal lattice. Thus, these grooves may be binding sites for hydrophobic peptides or other ligands.

Systhesis, Characterization and Spectroscopic Properties of (2E,6E)-2,6-Bis(2,3,4-tri-methoxy-benzylidene)cyclohexanone

2011 ◽  
Vol 396-398 ◽  
pp. 2338-2341
Author(s):  
Xing Chuan Wei ◽  
Zhi Li Liu ◽  
Kun Zhang ◽  
Zhi Yun Du ◽  
Xi Zheng
Keyword(s):  
Crystal Structure ◽  
Acetic Acid ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Spectroscopic Properties ◽  
Spectral Studies ◽  
Double Bonds ◽  
X Ray ◽  
Π Interactions ◽  
X Ray Crystallography

In this paper, (2E,6E)-2,6-Bis(2,3,4-tri-methoxy -benzylidene)cyclohexanone (omitted as tmbcho) (1) was obtained by the reaction of acetic acid, tetrahydrofuran, cyclohexanone and 2,3,4-tri-methoxy-benzaldehyde. Three non-classic hydrogen bonds were observed in the compound. X-ray crystallography shows that the crystal structure is stabilized by intermolecular C-H•••π interactions and it contains plenty of conjugated double bonds. The title compound was characterized by UV-vis and fluorescent spectral studies.

Triazene derivatives of (1,x-)diazacycloalkanes. Part VI. 3-({5,5-Dimethyl-3-[2-aryl-1-diazenyl]-1-imidazolidinyl}methyl)-4,4-dimethyl-1-[2-aryl-1-diazenyl]imidazolidines — Synthesis, characterization, and X-ray crystal structure

2006 ◽  
Vol 84 (10) ◽  
pp. 1294-1300 ◽  
Author(s):  
Keith Vaughan ◽  
Shasta Lee Moser ◽  
Reid Tingley ◽  
M Brad Peori ◽  
Valerio Bertolasi
Keyword(s):  
Crystal Structure ◽  
Significant Degree ◽  
Ion Trapping ◽  
Published Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Diazonium Ion ◽  
Derivatives Of ◽  
C Nmr

Reaction of a series of diazonium salts with a mixture of formaldehyde and 1,2-diamino-2-methylpropane affords the 3-({5,5-dimethyl-3-[2-aryl-1-diazenyl]-1-imidazolidinyl}methyl)-4,4-dimethyl-1-[2-aryl-1-diazenyl]imidazolidines (1a–1f) in excellent yield. The products have been characterized by IR and NMR spectroscopic analysis, elemental analysis, and X-ray crystallography. The X-ray crystal structure of the p-methoxycarbonyl derivative (1c) establishes without question the connectivity of these novel molecules, which can be described as linear bicyclic oligomers with two imidazolidinyl groups linked together by a one-carbon spacer. This is indeed a rare molecular building block. The molecular structure is corroborated by 1H and 13C NMR data, which correlates with the previously published data of compounds of types 5 and 6 derived from 1,3-propanediamine. The triazene moieties in the crystal of 1c display significant π conjugation, which gives the N—N bond a significant degree of double-bond character. This in turn causes restricted rotation around the N—N bond, which leads to considerable broadening of signals in both the 1H and 13C NMR spectra. The molecular ion of the p-cyanophenyl derivative (1b) was observed using electrospray mass spectrometry (ES + Na). The mechanism of formation of molecules of type 1 is proposed to involve diazonium ion trapping of the previously unreported bisimidazolidinyl methane (13).Key words: triazene, bistriazene, imidazolidine, synthesis, X-ray crystallography, NMR spectroscopy.

Crystal Structure, Spectroscopic and Redox Properties of Copper(II) Bis{2-[(2,6-dimethylphenyl)iminomethyl-3-methoxyphenolate]}

2007 ◽  
Vol 62 (9) ◽  
pp. 1133-1138 ◽  
Author(s):  
Veli T. Kasumov ◽  
Ibrahim Uçar ◽  
Ahmet Bulut ◽  
Fevzi Kösal
Keyword(s):  
Crystal Structure ◽  
Title Complex ◽  
Redox Properties ◽  
Orthorhombic Space Group ◽  
Long Distance ◽  
X Ray ◽  
X Ray Crystallography ◽  
Square Planar ◽  
Planar Molecules ◽  
Exchange Interaction Parameter

The coordination chemistry of N-(2,6-di-methylphenyl)-2-hydroxy-3-methoxybenzaldimine (1) with Cu(II) has been investigated by X-ray crystallography, electronic and EPR spectroscopies, as well as by electro- and magnetochemistry. The title complex 2 crystallizes in the orthorhombic space group P212121 (a = 8.1538, b = 17.7466, c =19.8507 Å). The mononuclear square-planar molecules 2 featuring trans-N2O2 coordination are connected via weak intermolecular C-H· · ·π interactions into infinite chains parallel to the a axis. Although the intermolecular Cu· · ·Cu separations within individual chains and between chains are very long (8.154 and 9.726 Å ), the exchange interaction parameter G = 2.03 < 4, estimated from solid state EPR spectra, suggests the existence of long-distance superexchange pathways between adjacent Cu(II) centers. The electronic and electrochemical features of the compound are also discussed.

scholarly journals Synthesis, Crystal Structure and Magnetic Behaviour of Dimeric and Polymeric Gadolinium Trifluoroacetate Complexes

2006 ◽  
Vol 61 (6) ◽  
pp. 699-707 ◽  
Author(s):  
Daniela John ◽  
Alexander Rohde ◽  
Werner Urland
Keyword(s):  
Crystal Structure ◽  
Magnetic Behaviour ◽  
Magnetic Data ◽  
Space Group ◽  
X Ray ◽  
Lattice Constants ◽  
Temperature Range ◽  
X Ray Crystallography ◽  
Carboxylate Groups

The gadolinium(III) trifluoroacetates ((CH3)2NH2)[Gd(CF3COO)4] (1), ((CH3)3NH)[Gd(CF3 COO)4(H2O)] (2), Gd(CF3COO)3(H2O)3 (3) as well as Gd2(CF3COO)6(H2O)2(phen)3 · C2H5OH (4) (phen = 1,10-phenanthroline) were synthesized and structurally characterized by X-ray crystallography. These compounds crystallize in the space group P1̅ (No. 2, Z = 2) (1, 2 and 4) and P 21/c (No. 14, Z = 4) (3), respectively, with the following lattice constants 1: a = 884.9(2), b = 1024.9(2), c = 1173.1(2) pm, α = 105.77(2), β = 99.51(2), γ = 107.93(2)°; 2: a = 965.1(1), b = 1028.6(1), c = 1271.3(2) pm, α = 111.83(2), β = 111.33(2), γ = 90.44(2)°; 3: a = 919.6(2), b = 1890.6(4), c = 978.7(2) pm, β = 113.94(2)°; 4: a = 1286.7(8), b = 1639.3(8), c = 1712.2(9) pm, α = 62.57(6), β = 84.13(5), γ = 68.28(5)°. The compounds consist of Gd3+ ions which are bridged by carboxylate groups either to chains (1 and 2) or to dimers (3 and 4). In addition to the Gd3+ dimers, compound (4) also contains monomeric Gd3+ units. The magnetic behaviour of 2 and 3 was investigated in a temperature range of 1.77 to 300 K. The magnetic data for these compounds indicate weak antiferromagnetic interactions

The crystal structure of ethyl-Z-3-amino-2-benzoyl-2-butenoate and measurement of the barrier to E,Z-isomerization

1980 ◽  
Vol 58 (17) ◽  
pp. 1821-1828 ◽  
Author(s):  
Gary D. Fallon ◽  
Bryan M. Gatehouse ◽  
Allan Pring ◽  
Ian D. Rae ◽  
Josephine A. Weigold
Keyword(s):  
Crystal Structure ◽  
Nuclear Magnetic Resonance ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Magnetic Resonance ◽  
Energy Of Activation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Free Energy Of Activation ◽  
Nuclear Magnetic

Ethyl-3-amino-2-benzoyl-2-butenoate crystallizes from pentane as either the E (mp 82–84 °C) or the Z-isomer (mp 95.5–96.5 °C). The E isomer is less stable, and changes spontaneously into the Z, which bas been identified by X-ray crystallography. The structure is characterised by an N–H/ester CO hydrogen bond and a very long C2—C3 bond (1.39 Å). Nuclear magnetic resonance methods have been used to measure the rate of [Formula: see text] isomerization at several temperatures, leading to the estimate that the free energy of activation at 268 K is 56 ± 8 kJ.

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