The Role of Cytochrome 2B1 Substrate Recognition Site Residues 115, 294, 297, 298, and 362 in the Oxidation of Steroids and 7-Alkoxycoumarins

2001 ◽  
Vol 394 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Tammy L. Domanski ◽  
You-Qun He ◽  
Emily E. Scott ◽  
Qinmi Wang ◽  
James R. Halpert
Keyword(s):  
Substrate Recognition ◽  
Recognition Site

Role of active site arginine residues in substrate recognition by PPM1A

2021 ◽  
Author(s):  
Itsumi Tani ◽  
Shogo Ito ◽  
Yukiko Shirahata ◽  
Yutaka Matsuyama ◽  
James G. Omichinski ◽  
...  
Keyword(s):  
Active Site ◽  
Substrate Recognition ◽  
Arginine Residues

scholarly journals Molecular Basis of Substrate Recognition of Endonuclease Q from the Euryarchaeon Pyrococcus furiosus

2019 ◽  
Vol 202 (2) ◽  
Author(s):  
Miyako Shiraishi ◽  
Shigenori Iwai
Keyword(s):  
Dna Repair ◽  
Bacillus Subtilis ◽  
Substrate Specificity ◽  
Molecular Basis ◽  
Pyrococcus Furiosus ◽  
Substrate Recognition ◽  
Base Flipping ◽  
Content Type ◽  
Cleavage Activity

ABSTRACT Endonuclease Q (EndoQ), a DNA repair endonuclease, was originally identified in the hyperthermophilic euryarchaeon Pyrococcus furiosus in 2015. EndoQ initiates DNA repair by generating a nick on DNA strands containing deaminated bases and an abasic site. Although EndoQ is thought to be important for maintaining genome integrity in certain bacteria and archaea, the underlying mechanism catalyzed by EndoQ remains unclear. Here, we provide insights into the molecular basis of substrate recognition by EndoQ from P. furiosus (PfuEndoQ) using biochemical approaches. Our results of the substrate specificity range and the kinetic properties of PfuEndoQ demonstrate that PfuEndoQ prefers the imide structure in nucleobases along with the discovery of its cleavage activity toward 5,6-dihydrouracil, 5-hydroxyuracil, 5-hydroxycytosine, and uridine in DNA. The combined results for EndoQ substrate binding and cleavage activity analyses indicated that PfuEndoQ flips the target base from the DNA duplex, and the cleavage activity is highly dependent on spontaneous base flipping of the target base. Furthermore, we find that PfuEndoQ has a relatively relaxed substrate specificity; therefore, the role of EndoQ in restriction modification systems was explored. The activity of the EndoQ homolog from Bacillus subtilis was found not to be inhibited by the uracil glycosylase inhibitor from B. subtilis bacteriophage PBS1, whose genome is completely replaced by uracil instead of thymine. Our findings suggest that EndoQ not only has additional functions in DNA repair but also could act as an antiviral enzyme in organisms with EndoQ. IMPORTANCE Endonuclease Q (EndoQ) is a lesion-specific DNA repair enzyme present in certain bacteria and archaea. To date, it remains unclear how EndoQ recognizes damaged bases. Understanding the mechanism of substrate recognition by EndoQ is important to grasp genome maintenance systems in organisms with EndoQ. Here, we find that EndoQ from the euryarchaeon Pyrococcus furiosus recognizes the imide structure in nucleobases by base flipping, and the cleavage activity is enhanced by the base pair instability of the target base, along with the discovery of its cleavage activity toward 5,6-dihydrouracil, 5-hydroxyuracil, 5-hydroxycytosine, and uridine in DNA. Furthermore, a potential role of EndoQ in Bacillus subtilis as an antiviral enzyme by digesting viral genome is demonstrated.

Critical role of a conserved transmembrane lysine in substrate recognition by the proton-coupled oligopeptide transporter YjdL

2014 ◽  
Vol 55 ◽  
pp. 311-317 ◽  
Author(s):  
Johanne M. Jensen ◽  
Nanda G. Aduri ◽  
Bala K. Prabhala ◽  
Rasmus Jahnsen ◽  
Henrik Franzyk ◽  
...  
Keyword(s):  
Substrate Recognition ◽  
Critical Role ◽  
Oligopeptide Transporter

The role of Arg-96 in Danio rerio creatine kinase in substrate recognition and active center configuration

2009 ◽  
Vol 44 (5) ◽  
pp. 413-418 ◽  
Author(s):  
Kouji Uda ◽  
Ai Kuwasaki ◽  
Kanami Shima ◽  
Tamotsu Matsumoto ◽  
Tomohiko Suzuki
Keyword(s):  
Creatine Kinase ◽  
Active Center ◽  
Danio Rerio ◽  
Substrate Recognition ◽  
Center Configuration

scholarly journals New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Louise Lassalle ◽  
Sylvain Engilberge ◽  
Dominique Madern ◽  
Pierre Vauclare ◽  
Bruno Franzetti ◽  
...  
Keyword(s):  
Renal Failure ◽  
Active Site ◽  
Ternary Complex ◽  
Substrate Recognition ◽  
Binding Mode ◽  
X Ray ◽  
Hyperoxaluria Type

Abstract Glyoxylate accumulation within cells is highly toxic. In humans, it is associated with hyperoxaluria type 2 (PH2) leading to renal failure. The glyoxylate content within cells is regulated by the NADPH/NADH dependent glyoxylate/hydroxypyruvate reductases (GRHPR). These are highly conserved enzymes with a dual activity as they are able to reduce glyoxylate to glycolate and to convert hydroxypyruvate into D-glycerate. Despite the determination of high-resolution X-ray structures, the substrate recognition mode of this class of enzymes remains unclear. We determined the structure at 2.0 Å resolution of a thermostable GRHPR from Archaea as a ternary complex in the presence of D-glycerate and NADPH. This shows a binding mode conserved between human and archeal enzymes. We also determined the first structure of GRHPR in presence of glyoxylate at 1.40 Å resolution. This revealed the pivotal role of Leu53 and Trp138 in substrate trafficking. These residues act as gatekeepers at the entrance of a tunnel connecting the active site to protein surface. Taken together, these results allowed us to propose a general model for GRHPR mode of action.

scholarly journals Role of substrate recognition in modulating strigolactone receptor selectivity in witchweed

2021 ◽  
pp. 101092
Author(s):  
Jiming Chen ◽  
Alexandra White ◽  
David C. Nelson ◽  
Diwakar Shukla
Keyword(s):  
Substrate Recognition ◽  
Receptor Selectivity
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