Crystal structure of cholesterol oxidase complexed with a steroid substrate: Implications for flavin adenine dinucleotide dependent alcohol oxidases

Biochemistry ◽  
1993 ◽  
Vol 32 (43) ◽  
pp. 11507-11515 ◽  
Author(s):  
Jiayao Li ◽  
Alice Vrielink ◽  
Peter Brick ◽  
David M. Blow
Keyword(s):  
Crystal Structure ◽  
Flavin Adenine Dinucleotide ◽  
Cholesterol Oxidase ◽  
Steroid Substrate

scholarly journals Crystal Structure of the Active Site Mutant Form of Soluble Fumarate Reductase, Osm1

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 504 ◽  
Author(s):  
Kim ◽  
Kwon ◽  
Jung ◽  
Chun ◽  
Ha ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Flavin Adenine Dinucleotide ◽  
Structural Information ◽  
Redox Balance ◽  
Underlying Mechanism ◽  
Fumarate Reductase ◽  
Mutant Form ◽  
Characteristic Features ◽  
Fad Binding

Soluble fumarate reductase is essential for survival under anaerobic conditions. This enzyme can maintain the redox balance in the cell by catalyzing the reduction of fumarate to succinate. Although the overall reaction mechanism of soluble fumarate reductase in yeast, Osm1, has been proposed by a previous structural study, the details of the underlying mechanism are not completely elucidated. The present study provides the structural information regarding the active site mutant form of Osm1 (R326A), thus, revealing that R326A mutation does not affect the substrate binding. Structural alterations of the residues surrounding the active site, and the missing 2nd flavin adenine dinucleotide (FAD) in the previously defined 2nd FAD binding site, were observed as characteristic features of the Osm1 R326A crystal structure. Based on these findings, we provided a clue that can explain the loss of activity of Osm1 R326A.

scholarly journals The crystal structure of AbsH3 : A putative flavin adenine dinucleotide‐dependent reductase in the abyssomicin biosynthesis pathway

2020 ◽  
Vol 89 (1) ◽  
pp. 132-137
Author(s):  
Jonathan A. Clinger ◽  
Xiachang Wang ◽  
Wenlong Cai ◽  
Yanyan Zhu ◽  
Mitchell D. Miller ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Flavin Adenine Dinucleotide ◽  
Biosynthesis Pathway

scholarly journals Structural Basis for Different Substrate Specificities of Two ADP-Ribose Pyrophosphatases from Thermus thermophilus HB8

2007 ◽  
Vol 190 (3) ◽  
pp. 1108-1117 ◽  
Author(s):  
Taisuke Wakamatsu ◽  
Noriko Nakagawa ◽  
Seiki Kuramitsu ◽  
Ryoji Masui
Keyword(s):  
Crystal Structure ◽  
Flavin Adenine Dinucleotide ◽  
Thermus Thermophilus ◽  
High Specificity ◽  
Ternary Complexes ◽  
Structural Basis ◽  
Water Molecules ◽  
Substrate Specificities ◽  
Catalytic Mechanisms

ABSTRACT ADP-ribose (ADPR) is one of the main substrates of Nudix proteins. Among the eight Nudix proteins of Thermus thermophilus HB8, we previously determined the crystal structure of Ndx4, an ADPR pyrophosphatase (ADPRase). In this study we show that Ndx2 of T. thermophilus also preferentially hydrolyzes ADPR and flavin adenine dinucleotide and have determined its crystal structure. We have determined the structures of Ndx2 alone and in complex with Mg2+, with Mg2+ and AMP, and with Mg2+ and a nonhydrolyzable ADPR analogue. Although Ndx2 recognizes the AMP moiety in a manner similar to those for other ADPRases, it recognizes the terminal ribose in a distinct manner. The residues responsible for the recognition of the substrate in Ndx2 are not conserved among ADPRases. This may reflect the diversity in substrate specificity among ADPRases. Based on these results, we propose the classification of ADPRases into two types: ADPRase-I enzymes, which exhibit high specificity for ADPR; and ADPRase-II enzymes, which exhibit low specificity for ADPR. In the active site of the ternary complexes, three Mg2+ ions are coordinated to the side chains of conserved glutamate residues and water molecules. Substitution of Glu90 and Glu94 with glutamine suggests that these residues are essential for catalysis. These results suggest that ADPRase-I and ADPRase-II enzymes have nearly identical catalytic mechanisms but different mechanisms of substrate recognition.

scholarly journals Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs

2020 ◽  
Vol 48 (12) ◽  
pp. 6788-6798 ◽  
Author(s):  
Sunny Sharma ◽  
Ewa Grudzien-Nogalska ◽  
Keith Hamilton ◽  
Xinfu Jiao ◽  
Jun Yang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Nicotinamide Adenine Dinucleotide ◽  
Mammalian Cells ◽  
Flavin Adenine Dinucleotide ◽  
Nicotinamide Adenine ◽  
Nudix Hydrolase ◽  
Decapping Enzymes ◽  
Hydrolysis Of ◽  
In Cells

Abstract We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5′caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins—Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.

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