Rational backbone redesign of a fructosyl peptide oxidase to widen its active site access tunnel

2020 ◽  
Vol 117 (12) ◽  
pp. 3688-3698
Author(s):  
Federica Rigoldi ◽  
Stefano Donini ◽  
Archimede Torretta ◽  
Anna Carbone ◽  
Alberto Redaelli ◽  
...  
Keyword(s):  
Active Site ◽  
Site Access ◽  
Fructosyl Peptide Oxidase

Conformation analysis of a surface loop that controls active site access in the GH11 xylanase A from Bacillus subtilis

2011 ◽  
Vol 18 (4) ◽  
pp. 1473-1479 ◽  
Author(s):  
Davi Serradella Vieira ◽  
Richard John Ward
Keyword(s):  
Bacillus Subtilis ◽  
Active Site ◽  
Conformation Analysis ◽  
Surface Loop ◽  
Site Access

scholarly journals Structure of theS. aureusPI-Specific Phospholipase C Reveals Modulation of Active Site Access by a Titratable π-Cation Latched Loop

Biochemistry ◽  
2012 ◽  
Vol 51 (12) ◽  
pp. 2579-2587 ◽  
Author(s):  
Rebecca Goldstein ◽  
Jiongjia Cheng ◽  
Boguslaw Stec ◽  
Mary F. Roberts
Keyword(s):  
Phospholipase C ◽  
Active Site ◽  
Site Access

Tryptophan 80 and Leucine 143 Are Critical for the Hydride Transfer Step of Thymidylate Synthase by Controlling Active Site Access†,‡

Biochemistry ◽  
2002 ◽  
Vol 41 (22) ◽  
pp. 7021-7029 ◽  
Author(s):  
Timothy A. Fritz ◽  
Lu Liu ◽  
Janet S. Finer-Moore ◽  
Robert M. Stroud
Keyword(s):  
Thymidylate Synthase ◽  
Active Site ◽  
Hydride Transfer ◽  
Transfer Step ◽  
Site Access

A survey of active site access channels in cytochromes P450

2004 ◽  
Vol 98 (7) ◽  
pp. 1175-1182 ◽  
Author(s):  
Rebecca C Wade ◽  
Peter J Winn ◽  
Ilme Schlichting ◽  
Sudarko
Keyword(s):  
Active Site ◽  
Cytochromes P450 ◽  
Site Access

Structural and dynamic basis of acid amido synthetase GH3.1: an investigation of substrate selectivity and major active site access channels

2015 ◽  
Vol 11 (3) ◽  
pp. 809-818 ◽  
Author(s):  
Xue Wang ◽  
Juan Du ◽  
Xiaojun Yao
Keyword(s):  
Active Site ◽  
Substrate Selectivity ◽  
Site Access

Investigation for substrate selectivity and active site access channels of GH3.1, a critical enzyme involved in modulating levels of cellular auxins/IAA.

Structural and Dynamic Basis of Human Cytochrome P450 7B1: A Survey of Substrate Selectivity and Major Active Site Access Channels

2012 ◽  
Vol 19 (2) ◽  
pp. 549-557 ◽  
Author(s):  
Ying-Lu Cui ◽  
Ji-Long Zhang ◽  
Qing-Chuan Zheng ◽  
Rui-Juan Niu ◽  
Yu Xu ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Active Site ◽  
Substrate Selectivity ◽  
Human Cytochrome ◽  
Site Access

Locating Al in the DABCO catalyst before and after Al extraction

1990 ◽  
Vol 48 (4) ◽  
pp. 265-267
Author(s):  
Kathleen B. Reuter
Keyword(s):  
Active Site ◽  
Inverse Relationship ◽  
Transverse Direction ◽  
Reaction Rate ◽  
Acid Phosphate ◽  
Fracture Surfaces ◽  
Al Content ◽  
Before And After ◽  
Relationship Of

The reaction rate and efficiency of piperazine to 1,4-diazabicyclo-octane (DABCO) depends on the Si/Al ratio of the MFI topology catalysts. The Al was shown to be the active site, however, in the Si/Al range of 30-200 the reaction rate increases as the Si/Al ratio increases. The objective of this work was to determine the location and concentration of Al to explain this inverse relationship of Al content with reaction rate.Two silicalite catalysts in the form of 1/16 inch SiO2/Al2O3 bonded extrudates were examined: catalyst A with a Si/Al of 83; and catalyst B, the acid/phosphate Al extracted form of catalyst A, with a Si/Al of 175. Five extrudates from each catalyst were fractured in the transverse direction and particles were obtained from the fracture surfaces near the center of the extrudate diameter. Particles were also obtained from the outside surfaces of five extrudates.

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

Contributions of the substrate-binding arginine residues to maleate-induced closure of the active site of Escherichia coli aspartate aminotransferase

2001 ◽  
Vol 268 (6) ◽  
pp. 1640-1645
Author(s):  
Annelise Matharu ◽  
Hideyuki Hayashi ◽  
Hiroyuki Kagamiyama ◽  
Bruno Maras ◽  
Robert A. John
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Aspartate Aminotransferase ◽  
Substrate Binding ◽  
Arginine Residues

Alkane upgrading effected by silica-supported pincer-iridium catalysts: Evidence of a shared active site with solution-phase species

2020 ◽  
Author(s):  
Alan Goldman ◽  
Boris Sheludko ◽  
Fuat Celik ◽  
Cristina Castro
Keyword(s):  
Active Site ◽  
Solution Phase ◽  
Iridium Catalysts
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