scholarly journals Crystal structures of two monomeric triosephosphate isomerase variants identifiedviaa directed-evolution protocol selecting forL-arabinose isomerase activity

2016 ◽  
Vol 72 (6) ◽  
pp. 490-499
Author(s):  
Mirja Krause ◽  
Tiila-Riikka Kiema ◽  
Peter Neubauer ◽  
Rik K. Wierenga
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Directed Evolution ◽  
Crystal Structures ◽  
Active Site ◽  
Triosephosphate Isomerase ◽  
Point Mutations ◽  
Van Der Waals Interactions ◽  
Side Chain ◽  
Arabinose Isomerase

The crystal structures are described of two variants of A-TIM: Ma18 (2.7 Å resolution) and Ma21 (1.55 Å resolution). A-TIM is a monomeric loop-deletion variant of triosephosphate isomerase (TIM) which has lost the TIM catalytic properties. Ma18 and Ma21 were identified after extensive directed-evolution selection experiments using anEscherichia coliL-arabinose isomerase knockout strain expressing a randomly mutated A-TIM gene. These variants facilitate better growth of theEscherichia coliselection strain in medium supplemented with 40 mML-arabinose. Ma18 and Ma21 differ from A-TIM by four and one point mutations, respectively. Ma18 and Ma21 are more stable proteins than A-TIM, as judged from CD melting experiments. Like A-TIM, both proteins are monomeric in solution. In the Ma18 crystal structure loop 6 is open and in the Ma21 crystal structure loop 6 is closed, being stabilized by a bound glycolate molecule. The crystal structures show only small differences in the active site compared with A-TIM. In the case of Ma21 it is observed that the point mutation (Q65L) contributes to small structural rearrangements near Asn11 of loop 1, which correlate with different ligand-binding properties such as a loss of citrate binding in the active site. The Ma21 structure also shows that its Leu65 side chain is involved in van der Waals interactions with neighbouring hydrophobic side-chain moieties, correlating with its increased stability. The experimental data suggest that the increased stability and solubility properties of Ma21 and Ma18 compared with A-TIM cause better growth of the selection strain when coexpressing Ma21 and Ma18 instead of A-TIM.

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.

scholarly journals How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dariusz Czernecki ◽  
Pierre Legrand ◽  
Mustafa Tekpinar ◽  
Sandrine Rosario ◽  
Pierre-Alexandre Kaminski ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Active Site ◽  
Metal Ion ◽  
Restriction Endonucleases ◽  
Structural Element

AbstractBacteriophages have long been known to use modified bases in their DNA to prevent cleavage by the host’s restriction endonucleases. Among them, cyanophage S-2L is unique because its genome has all its adenines (A) systematically replaced by 2-aminoadenines (Z). Here, we identify a member of the PrimPol family as the sole possible polymerase of S-2L and we find it can incorporate both A and Z in front of a T. Its crystal structure at 1.5 Å resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (DatZ), that leaves intact all other dNTPs, including dZTP. This explains the absence of A in S-2L genome. Crystal structures of DatZ with various ligands, including one at sub-angstrom resolution, allow to describe its mechanism as a typical two-metal-ion mechanism and to set the stage for its engineering.

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.

The adaptability of the active site of trypanosomal triosephosphate isomerase as observed in the crystal structures of three different complexes

1991 ◽  
Vol 10 (1) ◽  
pp. 50-69 ◽  
Author(s):  
Martin E. M. Noble ◽  
Rik K. Wierenga ◽  
Anne-Marie Lambeir ◽  
Fred R. Opperdoes ◽  
Andy-Mark W. H. Thunnissen ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Active Site ◽  
Triosephosphate Isomerase

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.

scholarly journals Structural Analysis of The OXA-48 Carbapenemase Bound to A “Poor” Carbapenem Substrate, Doripenem

Antibiotics ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 145 ◽  
Author(s):  
Krisztina M. Papp-Wallace ◽  
Vijay Kumar ◽  
Elise T. Zeiser ◽  
Scott A. Becka ◽  
Focco van den Akker
Keyword(s):  
Public Health ◽  
Crystal Structure ◽  
Salt Bridge ◽  
Hydrolytic Activity ◽  
Van Der Waals Interactions ◽  
Side Chain ◽  
Carbapenem Resistant ◽  
Mechanistic Basis ◽  
Further Development ◽  
Carbapenem Resistant Enterobacteriaceae

Carbapenem-resistant Enterobacteriaceae are a significant threat to public health, and a major resistance determinant that promotes this phenotype is the production of the OXA-48 carbapenemase. The activity of OXA-48 towards carbapenems is a puzzling phenotype as its hydrolytic activity against doripenem is non-detectable. To probe the mechanistic basis for this observation, we determined the 1.5 Å resolution crystal structure of the deacylation deficient K73A variant of OXA-48 in complex with doripenem. Doripenem is observed in the Δ1R and Δ1S tautomeric states covalently attached to the catalytic S70 residue. Likely due to positioning of residue Y211, the carboxylate moiety of doripenem is making fewer hydrogen bonding/salt-bridge interactions with R250 compared to previously determined carbapenem OXA structures. Moreover, the hydroxyethyl side chain of doripenem is making van der Waals interactions with a key V120 residue, which likely affects the deacylation rate of doripenem. We hypothesize that positions V120 and Y211 play important roles in the carbapenemase profile of OXA-48. Herein, we provide insights for the further development of the carbapenem class of antibiotics that could render them less effective to hydrolysis by or even inhibit OXA carbapenemases.

scholarly journals Crystal structures of the editing domain of Escherichia coli leucyl-tRNA synthetase and its complexes with Met and Ile reveal a lock-and-key mechanism for amino acid discrimination

2006 ◽  
Vol 394 (2) ◽  
pp. 399-407 ◽  
Author(s):  
Yunqing Liu ◽  
Jing Liao ◽  
Bin Zhu ◽  
En-Duo Wang ◽  
Jianping Ding
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Crystal Structures ◽  
Active Site ◽  
Binding Pocket ◽  
Trna Synthetase ◽  
Vital Role ◽  
Common Mechanism ◽  
Trna Synthetases ◽  
Editing Domain

aaRSs (aminoacyl-tRNA synthetases) are responsible for the covalent linking of amino acids to their cognate tRNAs via the aminoacylation reaction and play a vital role in maintaining the fidelity of protein synthesis. LeuRS (leucyl-tRNA synthetase) can link not only the cognate leucine but also the nearly cognate residues Ile and Met to tRNALeu. The editing domain of LeuRS deacylates the mischarged Ile–tRNALeu and Met–tRNALeu. We report here the crystal structures of ecLeuRS-ED (the editing domain of Escherichia coli LeuRS) in both the apo form and in complexes with Met and Ile at 2.0 Å, 2.4 Å, and 3.2 Å resolution respectively. The editing active site consists of a number of conserved amino acids, which are involved in the precise recognition and binding of the noncognate amino acids. The substrate-binding pocket has a rigid structure which has an optimal stereochemical fit for Ile and Met, but has steric hindrance for leucine. Based on our structural results and previously available biochemical data, we propose that ecLeuRS-ED uses a lock-and-key mechanism to recognize and discriminate between the amino acids. Structural comparison also reveals that all subclass Ia aaRSs share a conserved structure core consisting of the editing domain and conserved residues at the editing active site, suggesting that these enzymes may use a common mechanism for the editing function.

Structures of the PKC-ι kinase domain in its ATP-bound and apo forms reveal defined structures of residues 533–551 in the C-terminal tail and their roles in ATP binding

2010 ◽  
Vol 66 (5) ◽  
pp. 577-583 ◽  
Author(s):  
Tetsuo Takimura ◽  
Kenji Kamata ◽  
Kazuhiro Fukasawa ◽  
Hirokazu Ohsawa ◽  
Hideya Komatani ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Binding Pocket ◽  
Kinase Domain ◽  
Van Der Waals Interactions ◽  
Side Chain ◽  
Phosphoryl Transfer ◽  
Atp Binding ◽  
Cellular Functions ◽  
Substrate Complex ◽  
Wide Range

Protein kinase C (PKC) plays an essential role in a wide range of cellular functions. Although crystal structures of the PKC-θ, PKC-ι and PKC-βII kinase domains have previously been determined in complexes with small-molecule inhibitors, no structure of a PKC–substrate complex has been determined. In the previously determined PKC-ι complex, residues 533–551 in the C-terminal tail were disordered. In the present study, crystal structures of the PKC-ι kinase domain in its ATP-bound and apo forms were determined at 2.1 and 2.0 Å resolution, respectively. In the ATP complex, the electron density of all of the C-terminal tail residues was well defined. In the structure, the side chain of Phe543 protrudes into the ATP-binding pocket to make van der Waals interactions with the adenine moiety of ATP; this is also observed in other AGC kinase structures such as binary and ternary substrate complexes of PKA and AKT. In addition to this interaction, the newly defined residues around the turn motif make multiple hydrogen bonds to glycine-rich-loop residues. These interactions reduce the flexibility of the glycine-rich loop, which is organized for ATP binding, and the resulting structure promotes an ATP conformation that is suitable for the subsequent phosphoryl transfer. In the case of the apo form, the structure and interaction mode of the C-terminal tail of PKC-ι are essentially identical to those of the ATP complex. These results indicate that the protein structure is pre-organized before substrate binding to PKC-ι, which is different from the case of the prototypical AGC-branch kinase PKA.

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