Understanding substrate binding and the role of gatekeeping residues in PigC access tunnels

2021 ◽  
Author(s):  
Stefanie Brands ◽  
Jarno G. Sikkens ◽  
Mehdi D. Davari ◽  
Hannah U. C. Brass ◽  
Andreas S. Klein ◽  
...  
Keyword(s):  
Rational Design ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Short Chain ◽  
Substrate Binding Pocket

Prodigiosin ligase PigC has been engineered by semi-rational design to accept short chain-pyrroles, providing molecular understanding of access tunnels and the substrate-binding pocket.

Structure and function of Plasmodium falciparum malate dehydrogenase: Role of critical amino acids in co-substrate binding pocket

Biochimie ◽  
2009 ◽  
Vol 91 (11-12) ◽  
pp. 1509-1517 ◽  
Author(s):  
Anupam Pradhan ◽  
Abhai K. Tripathi ◽  
Prashant V. Desai ◽  
Prasenjit K. Mukherjee ◽  
Mitchell A. Avery ◽  
...  
Keyword(s):  
Amino Acids ◽  
Plasmodium Falciparum ◽  
Malate Dehydrogenase ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Structure And Function ◽  
Substrate Binding Pocket ◽  
And Function

Significant improvement to the catalytic properties of aspartate aminotransferase: Role of hydrophobic and charged residues in the substrate binding pocket

Biochemistry ◽  
1994 ◽  
Vol 33 (1) ◽  
pp. 90-97 ◽  
Author(s):  
Eleonore Koehler ◽  
Mark Seville ◽  
Joachim Jaeger ◽  
Ian Fotheringham ◽  
Michael Hunter ◽  
...  
Keyword(s):  
Aspartate Aminotransferase ◽  
Catalytic Properties ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Substrate Binding Pocket ◽  
Charged Residues

scholarly journals Role of a Conserved Membrane Glycine Residue in a Dicarboxylate Transporter from Sinorhizobium meliloti

2006 ◽  
Vol 189 (5) ◽  
pp. 2160-2163 ◽  
Author(s):  
Maria A. Trainer ◽  
Svetlana N. Yurgel ◽  
Michael L. Kahn
Keyword(s):  
Amino Acid ◽  
Sinorhizobium Meliloti ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Significant Activity ◽  
Nitrogen Fixing ◽  
Substrate Binding Pocket ◽  
Glycine Residue

ABSTRACT Nitrogen-fixing rhizobial bacteroids import dicarboxylates by using the DctA transporter. G114 of DctA is highly conserved. A G114D mutant is inactive, but DctA with a small amino acid (G114A) or a helix disrupter (G114P) retains significant activity. G114 probably interacts with other membrane helices in stabilizing a substrate-binding pocket.

scholarly journals Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yufei Han ◽  
Qian Zhuang ◽  
Bo Sun ◽  
Wenping Lv ◽  
Sheng Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Biochemical Characterization ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Substrate Binding Pocket ◽  
Transmembrane Segments ◽  
Therapeutic Molecules ◽  
Binding Cavity ◽  
Immune System Regulation ◽  
Mediated Reduction

AbstractSteroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-Δ4 structure, such as testosterone or progesterone, are catalyzed by steroid 5α-reductases (SRD5As) to generate their corresponding 3-oxo-5α steroids, which are essential for multiple physiological and pathological processes. SRD5A2 is already a target of clinically relevant drugs. However, the detailed mechanism of SRD5A-mediated reduction remains elusive. Here we report the crystal structure of PbSRD5A from Proteobacteria bacterium, a homolog of both SRD5A1 and SRD5A2, in complex with the cofactor NADPH at 2.0 Å resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic substrate binding cavity, whereas TM5-7 coordinate cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with biochemical characterization, define the substrate binding pocket of SRD5As, explain the properties of disease-related mutants and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-Δ4 reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible.

Characterization of the Acyl Substrate Binding Pocket of Acetyl-CoA Synthetase†

Biochemistry ◽  
2006 ◽  
Vol 45 (38) ◽  
pp. 11482-11490 ◽  
Author(s):  
Cheryl Ingram-Smith ◽  
Barrett I. Woods ◽  
Kerry S. Smith
Keyword(s):  
Substrate Binding ◽  
Binding Pocket ◽  
Substrate Binding Pocket ◽  
Acetyl Coa

scholarly journals Improving the Substrate Affinity and Catalytic Efficiency of β-Glucosidase Bgl3A from Talaromyces leycettanus JCM12802 by Rational Design

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1882
Author(s):  
Wei Xia ◽  
Yingguo Bai ◽  
Pengjun Shi
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Substrate Binding ◽  
Enzymatic Saccharification ◽  
Catalytic Efficiency ◽  
Binding Pocket ◽  
Glycoside Hydrolases ◽  
Cellulosic Biomass ◽  
Substrate Affinity ◽  
Hydrogen Bonding Networks

Improving the substrate affinity and catalytic efficiency of β-glucosidase is necessary for better performance in the enzymatic saccharification of cellulosic biomass because of its ability to prevent cellobiose inhibition on cellulases. Bgl3A from Talaromyces leycettanus JCM12802, identified in our previous work, was considered a suitable candidate enzyme for efficient cellulose saccharification with higher catalytic efficiency on the natural substrate cellobiose compared with other β-glucosidase but showed insufficient substrate affinity. In this work, hydrophobic stacking interaction and hydrogen-bonding networks in the active center of Bgl3A were analyzed and rationally designed to strengthen substrate binding. Three vital residues, Met36, Phe66, and Glu168, which were supposed to influence substrate binding by stabilizing adjacent binding site, were chosen for mutagenesis. The results indicated that strengthening the hydrophobic interaction between stacking aromatic residue and the substrate, and stabilizing the hydrogen-bonding networks in the binding pocket could contribute to the stabilized substrate combination. Four dominant mutants, M36E, M36N, F66Y, and E168Q with significantly lower Km values and 1.4–2.3-fold catalytic efficiencies, were obtained. These findings may provide a valuable reference for the design of other β-glucosidases and even glycoside hydrolases.

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