scholarly journals Crystal Structure of a Mini-intein Reveals a Conserved Catalytic Module Involved in Side Chain Cyclization of Asparagine during Protein Splicing

2003 ◽  
Vol 278 (40) ◽  
pp. 39133-39142 ◽  
Author(s):  
Yi Ding ◽  
Ming-Qun Xu ◽  
Inca Ghosh ◽  
Xuehui Chen ◽  
Sebastien Ferrandon ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Side Chain ◽  
Protein Splicing ◽  
Catalytic Module

Structural Studies on N-(2,4,6-Trimethylphenyl)-methyl/ chloro-acetamides, 2,4,6-(CH3)3C6H2NH-CO-CH3–yXy (X = CH3 or Cl and y = 0, 1, 2)

2006 ◽  
Vol 61 (10-11) ◽  
pp. 588-594 ◽  
Author(s):  
Basavalinganadoddy Thimme Gowda ◽  
Jozef Kožíšek ◽  
Hartmut Fuess
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structural Data ◽  
The Other ◽  
Side Chain ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
Lattice Constants ◽  
Peptide Linkage ◽  
The Mean

TMPAThe effect of substitutions in the ring and in the side chain on the crystal structure of N- (2,4,6-trimethylphenyl)-methyl/chloro-acetamides of the configuration 2,4,6-(CH3)3C6H2NH-COCH3− yXy (X = CH3 or Cl and y = 0,1, 2) has been studied by determining the crystal structures of N-(2,4,6-trimethylphenyl)-acetamide, 2,4,6-(CH3)3C6H2NH-CO-CH3 (); N-(2,4,6- trimethylphenyl)-2-methylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2-CH3 (TMPMA); N-(2,4,6- trimethylphenyl)-2,2-dimethylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH(CH3)2 (TMPDMA) and N-(2,4,6-trimethylphenyl)-2,2-dichloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CHCl2 (TMPDCA). The crystallographic system, space group, formula units and lattice constants in Å are: TMPA: monoclinic, Pn, Z = 2, a = 8.142(3), b = 8.469(3), c = 8.223(3), β = 113.61(2)◦; TMPMA: monoclinic, P21/n, Z = 8, a = 9.103(1), b = 15.812(2), c = 16.4787(19), α = 89.974(10)◦, β = 96.951(10)◦, γ =89.967(10)◦; TMPDMA: monoclinic, P21/c, Z = 4, a =4.757(1), b= 24.644(4), c =10.785(2), β = 99.647(17)◦; TMPDCA: triclinic, P¯1, Z = 2, a = 4.652(1), b = 11.006(1), c = 12.369(1), α = 82.521(7)◦, β = 83.09(1)◦, γ = 79.84(1)◦. The results are analyzed along with the structural data of N-phenylacetamide, C6H5NH-CO-CH3; N-(2,4,6-trimethylphenyl)-2-chloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)-acetamide, 2,4,6-Cl3C6H2NH-COCH3; N-(2,4,6-trichlorophenyl)-2-chloroacetamide, 2,4,6-Cl3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)- 2,2-dichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CHCl2 and N-(2,4,6-trichlorophenyl)- 2,2,2-trichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CCl3. TMPA, TMPMA and TMPDCA have one molecule each in their asymmetric units, while TMPDMA has two molecules in its asymmetric unit. Changes in the mean ring distances are smaller on substitution as the effect has to be transmitted through the peptide linkage. The comparison of the other bond parameters reveal that there are significant changes in them on substitution.

Crystal structure of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis

2021 ◽  
Vol 77 (11) ◽  
Author(s):  
Kohei Sasamoto ◽  
Tomoki Himiyama ◽  
Kunihiko Moriyoshi ◽  
Takashi Ohmoto ◽  
Koichi Uegaki ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cellulose Acetate ◽  
Electron Density ◽  
Active Site ◽  
Catalytic Domain ◽  
Crystal Packing ◽  
Signal Sequence ◽  
Industrial Applications ◽  
Side Chain ◽  
Active Site Conformation

The acetylxylan esterases (AXEs) classified into carbohydrate esterase family 4 (CE4) are metalloenzymes that catalyze the deacetylation of acetylated carbohydrates. AXE from Caldanaerobacter subterraneus subsp. tengcongensis (TTE0866), which belongs to CE4, is composed of three parts: a signal sequence (residues 1–22), an N-terminal region (NTR; residues 23–135) and a catalytic domain (residues 136–324). TTE0866 catalyzes the deacetylation of highly substituted cellulose acetate and is expected to be useful for industrial applications in the reuse of resources. In this study, the crystal structure of TTE0866 (residues 23–324) was successfully determined. The crystal diffracted to 1.9 Å resolution and belonged to space group I212121. The catalytic domain (residues 136–321) exhibited a (β/α)7-barrel topology. However, electron density was not observed for the NTR (residues 23–135). The crystal packing revealed the presence of an intermolecular space without observable electron density, indicating that the NTR occupies this space without a defined conformation or was truncated during the crystallization process. Although the active-site conformation of TTE0866 was found to be highly similar to those of other CE4 enzymes, the orientation of its Trp264 side chain near the active site was clearly distinct. The unique orientation of the Trp264 side chain formed a different-shaped cavity within TTE0866, which may contribute to its reactivity towards highly substituted cellulose acetate.

Family 7 cellobiohydrolases from Phanerochaete chrysosporium: crystal structure of the catalytic module of Cel7D (CBH58) at 1.32 Å resolution and homology models of the isozymes

2001 ◽  
Vol 314 (5) ◽  
pp. 1097-1111 ◽  
Author(s):  
Inés G Muñoz ◽  
Wimal Ubhayasekera ◽  
Hongbin Henriksson ◽  
Istvan Szabó ◽  
Göran Pettersson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Phanerochaete Chrysosporium ◽  
Catalytic Module ◽  
Homology Models

scholarly journals Crystal structure of ethyl (2S,2′R)-1′-benzyl-3-oxo-3H-dispiro[1-benzothiophene-2,3′-pyrrolidine-2′,11′′-indeno[1,2-b]quinoxaline]-4′-carboxylate

2015 ◽  
Vol 71 (3) ◽  
pp. o195-o196
Author(s):  
J. Govindaraj ◽  
R. Raja ◽  
M. Suresh ◽  
R. Raghunathan ◽  
A. SubbiahPandi
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Ring System ◽  
Side Chain ◽  
Dihedral Angles ◽  
Pyrrolidine Ring ◽  
Compound C ◽  
Dimensional Network ◽  
Centroid Distance ◽  
Quinoxaline Ring

In the title compound, C35H27N3O3S, the spiro-linked five-membered rings both adopt twisted conformations. The pyrrolidine ring makes dihedral angles of 80.5 (1) and 77.4 (9)° with the benzothiophene ring system and the quinoxaline ring system, respectively. The S atom and C=O unit of the benzothiophene ring system are disordered over two opposite orientations in a 0.768 (4):0.232 (4) ratio. The atoms of the ethyl side chain are disordered over two sets of sites in a 0.680 (16):0.320 (16) ratio. In the crystal, molecules are linked by C—H...O, C—H...N and π–π interactions [shortest centroid–centroid distance = 3.4145 (19) Å], resulting in a three-dimensional network.

scholarly journals Crystal Structure of the COMPASS H3K4 Methyltransferase Catalytic Module

Cell ◽  
2018 ◽  
Vol 174 (5) ◽  
pp. 1106-1116.e9 ◽  
Author(s):  
Peter L. Hsu ◽  
Heng Li ◽  
Ho-Tak Lau ◽  
Calvin Leonen ◽  
Abhinav Dhall ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Module

(3aS,5aR,6R,8aR)-3a-Hydroxy-5a-methyl-6-[(1R,2E,4R)-1,4,5-trimethyl-2-hexen-1-yl]-3a,4,5,5a,6,7,8,8a-octahydro-2H-cyclopenta[e]benzofuran-2-one

2007 ◽  
Vol 63 (11) ◽  
pp. o4196-o4196
Author(s):  
Wen-liang Wang ◽  
Hong-wen Tao ◽  
Wei Sun ◽  
Qian-Qun Gu ◽  
Wei-Ming Zhu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Absolute Configuration ◽  
Title Compound ◽  
Optical Rotation ◽  
Side Chain ◽  
Compound C ◽  
Extended Chain ◽  
Halotolerant Fungus ◽  
The Absolute

The title compound, C21H32O3, also known as dimethylincisterol A3, was isolated from halotolerant fungus THW-18. It is composed of three fused rings and a side chain. In the crystal structure, the molecules interact with each other via O—H...O hydrogen bonds, resulting in an extended chain along the b axis. The absolute configuration was assigned from the measured optical rotation and reference to the literature.

scholarly journals A substrate selected by phage display exhibits enhanced side-chain hydrogen bonding to HIV-1 protease

2018 ◽  
Vol 74 (7) ◽  
pp. 690-694 ◽  
Author(s):  
Ian W. Windsor ◽  
Ronald T. Raines
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Molecular Recognition ◽  
Hydrogen Bonds ◽  
Phage Display ◽  
Directed Evolution ◽  
Side Chain ◽  
Endogenous Substrates ◽  
Hiv 1 ◽  
Additional Hydrogen

Crystal structures of inactive variants of HIV-1 protease bound to peptides have revealed how the enzyme recognizes its endogenous substrates. The best of the known substrates is, however, a nonnatural substrate that was identified by directed evolution. The crystal structure of the complex between this substrate and the D25N variant of the protease is reported at a resolution of 1.1 Å. The structure has several unprecedented features, especially the formation of additional hydrogen bonds between the enzyme and the substrate. This work expands the understanding of molecular recognition by HIV-1 protease and informs the design of new substrates and inhibitors.

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