scholarly journals Structure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid and glutarate: insight into the basis of its substrate specificity

2001 ◽  
Vol 8 (12) ◽  
pp. 1253-1264 ◽  
Author(s):  
Youngsoo Kim ◽  
Wim G.J Hol
Keyword(s):  
Substrate Specificity ◽  
Cephalosporin Acylase ◽  
Insight Into

scholarly journals RNA-Seq Approach for Genetic Improvement of Meat Quality in Pig and Evolutionary Insight into the Substrate Specificity of Animal Carbonyl Reductases

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e42198 ◽  
Author(s):  
Won Yong Jung ◽  
Seul Gi Kwon ◽  
Minky Son ◽  
Eun Seok Cho ◽  
Yuno Lee ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Meat Quality ◽  
Genetic Improvement ◽  
Rna Seq ◽  
Insight Into

Structural insight into OprD substrate specificity

2007 ◽  
Vol 14 (11) ◽  
pp. 1108-1109 ◽  
Author(s):  
Shyamasri Biswas ◽  
Mohammad M Mohammad ◽  
Dimki R Patel ◽  
Liviu Movileanu ◽  
Bert van den Berg
Keyword(s):  
Substrate Specificity ◽  
Structural Insight ◽  
Insight Into

scholarly journals Probing the promiscuity of ent-kaurene oxidases via combinatorial biosynthesis

2016 ◽  
Vol 113 (9) ◽  
pp. 2526-2531 ◽  
Author(s):  
Sibongile Mafu ◽  
Meirong Jia ◽  
Jiachen Zi ◽  
Dana Morrone ◽  
Yisheng Wu ◽  
...  
Keyword(s):  
Natural Products ◽  
Metabolic Engineering ◽  
Substrate Specificity ◽  
Plant Hormone ◽  
Structural Similarity ◽  
Combinatorial Biosynthesis ◽  
Underlying Structure ◽  
Engineering System ◽  
Insight Into

The substrate specificity of enzymes from natural products’ metabolism is a topic of considerable interest, with potential biotechnological use implicit in the discovery of promiscuous enzymes. However, such studies are often limited by the availability of substrates and authentic standards for identification of the resulting products. Here, a modular metabolic engineering system is used in a combinatorial biosynthetic approach toward alleviating this restriction. In particular, for studies of the multiply reactive cytochrome P450, ent-kaurene oxidase (KO), which is involved in production of the diterpenoid plant hormone gibberellin. Many, but not all, plants make a variety of related diterpenes, whose structural similarity to ent-kaurene makes them potential substrates for KO. Use of combinatorial biosynthesis enabled analysis of more than 20 such potential substrates, as well as structural characterization of 12 resulting unknown products, providing some insight into the underlying structure–function relationships. These results highlight the utility of this approach for investigating the substrate specificity of enzymes from complex natural products’ biosynthesis.

Crystal Structures of 2-Methylisocitrate Lyase in Complex with Product and with Isocitrate Inhibitor Provide Insight into Lyase Substrate Specificity, Catalysis and Evolution†,‡

Biochemistry ◽  
2005 ◽  
Vol 44 (8) ◽  
pp. 2949-2962 ◽  
Author(s):  
Sijiu Liu ◽  
Zhibing Lu ◽  
Yin Han ◽  
Eugene Melamud ◽  
Debra Dunaway-Mariano ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Crystal Structures ◽  
Insight Into

scholarly journals Structural insight into substrate specificity of human intestinal maltase-glucoamylase

2011 ◽  
Vol 2 (10) ◽  
pp. 827-836 ◽  
Author(s):  
Limei Ren ◽  
Xiaohong Qin ◽  
Xiaofang Cao ◽  
Lele Wang ◽  
Fang Bai ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Structural Insight ◽  
Human Intestinal Maltase ◽  
Insight Into

scholarly journals Structural and evolutionary relationships of “AT-less” type I polyketide synthase ketosynthases

2015 ◽  
Vol 112 (41) ◽  
pp. 12693-12698 ◽  
Author(s):  
Jeremy R. Lohman ◽  
Ming Ma ◽  
Jerzy Osipiuk ◽  
Boguslaw Nocek ◽  
Youngchang Kim ◽  
...  
Keyword(s):  
Amino Acid ◽  
Substrate Specificity ◽  
Polyketide Synthase ◽  
Acyl Carrier Protein ◽  
Structural Diversity ◽  
Type I ◽  
Substrate Specificities ◽  
In Trans ◽  
Canonical Type ◽  
Insight Into

Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.

scholarly journals Altering the Substrate Specificity of Cephalosporin Acylase by Directed Evolution of the β-Subunit

2002 ◽  
Vol 277 (44) ◽  
pp. 42121-42127 ◽  
Author(s):  
Linda G. Otten ◽  
Charles F. Sio ◽  
Johanna Vrielink ◽  
Robbert H. Cool ◽  
Wim J. Quax
Keyword(s):  
Substrate Specificity ◽  
Directed Evolution ◽  
Β Subunit ◽  
Cephalosporin Acylase

scholarly journals Insight into the Binding and Hydrolytic Preferences of hNudt16 Based on Nucleotide Diphosphate Substrates

2021 ◽  
Vol 22 (20) ◽  
pp. 10929
Author(s):  
Magdalena Chrabąszczewska ◽  
Maria Winiewska-Szajewska ◽  
Natalia Ostrowska ◽  
Elżbieta Bojarska ◽  
Janusz Stępiński ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Substrate Specificity ◽  
Ligand Binding ◽  
Regulatory Role ◽  
Stacking Interactions ◽  
Binding Modes ◽  
Biological Functions ◽  
Insight Into ◽  
Potential Regulatory Role

Nudt16 is a member of the NUDIX family of hydrolases that show specificity towards substrates consisting of a nucleoside diphosphate linked to another moiety X. Several substrates for hNudt16 and various possible biological functions have been reported. However, some of these reports contradict each other and studies comparing the substrate specificity of the hNudt16 protein are limited. Therefore, we quantitatively compared the affinity of hNudt16 towards a set of previously published substrates, as well as identified novel potential substrates. Here, we show that hNudt16 has the highest affinity towards IDP and GppG, with Kd below 100 nM. Other tested ligands exhibited a weaker affinity of several orders of magnitude. Among the investigated compounds, only IDP, GppG, m7GppG, AppA, dpCoA, and NADH were hydrolyzed by hNudt16 with a strong substrate preference for inosine or guanosine containing compounds. A new identified substrate for hNudt16, GppG, which binds the enzyme with an affinity comparable to that of IDP, suggests another potential regulatory role of this protein. Molecular docking of hNudt16-ligand binding inside the hNudt16 pocket revealed two binding modes for representative substrates. Nucleobase stabilization by Π stacking interactions with His24 has been associated with strong binding of hNudt16 substrates.

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