55 Years of the Rossmann Fold

Aminoacyl-tRNA synthetases produce aminoacyl-tRNAs from the substrate tRNA and its cognate amino acid with the aid of ATP. Two types of glutamyl-tRNA synthetase (GluRS) have been discovered: discriminating GluRS (D-GluRS) and nondiscriminating GluRS (ND-GluRS). D-GluRS glutamylates tRNAGluonly, while ND-GluRS glutamylates both tRNAGluand tRNAGln. ND-GluRS produces the intermediate Glu-tRNAGln, which is converted to Gln-tRNAGlnby Glu-tRNAGlnamidotransferase. Two GluRS homologues fromThermotoga maritima, TM1875 and TM1351, have been biochemically characterized and it has been clarified that only TM1875 functions as an ND-GluRS. Furthermore, the crystal structure of theT. maritimaND-GluRS, TM1875, was determined in complex with a Glu-AMP analogue at 2.0 Å resolution. TheT. maritimaND-GluRS contains a characteristic structure in the connective-peptide domain, which is inserted into the catalytic Rossmann-fold domain. The glutamylation ability of tRNAGlnby ND-GluRS was measured in the presence of the bacterial Glu-tRNAGlnamidotransferase GatCAB. Interestingly, the glutamylation efficiency was not affected even in the presence of excess GatCAB. Therefore, GluRS avoids competition with GatCAB and glutamylates tRNAGln.

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On the diversity of F420-dependent oxidoreductases: a sequence- and structure-based classification

10.1101/2020.08.24.261826 ◽

2020 ◽

Author(s):

María Laura Mascotti ◽

Maximiliano Juri Ayub ◽

Marco W. Fraaije

Keyword(s):

Evolutionary Analysis ◽

Structural Homology ◽

Structural Variability ◽

Rossmann Fold ◽

Tim Barrel

AbstractThe F420 deazaflavin cofactor is an intriguing molecule as it structurally resembles the canonical flavin cofactor, although biochemically behaves as a nicotinamide cofactor. Since its discovery, numerous enzymes relying on it have been described. The known deazaflavoproteins are taxonomically restricted to Archaea and Bacteria. The biochemistry of the deazaflavoenzymes is diverse and they exhibit some degree of structural variability as well. In this study a thorough sequence and structural homology evolutionary analysis was performed in order to generate an overarching classification of all known F420-dependent oxidoreductases. Five different superfamilies are described: Superfamily I, TIM-barrel F420-dependent enzymes; Superfamily II, Rossmann fold F420-dependent enzymes; Superfamily III, β-roll F420-dependent enzymes; Superfamily IV, SH3 barrel F420-dependent enzymes and Superfamily V, 3 layer ββα sandwich F420-dependent enzymes. This classification aims to be the framework for the identification, the description and the understanding the biochemistry of novel deazaflavoenzymes.

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Rossmann Fold

Encyclopedia of Genetics, Genomics, Proteomics and Informatics ◽

10.1007/978-1-4020-6754-9_14877 ◽

2008 ◽

pp. 1742-1742

Keyword(s):

Rossmann Fold

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Rossmann-Fold Methyltransferases: Taking a “β-Turn” around Their Cofactor, S-Adenosylmethionine

Biochemistry ◽

10.1021/acs.biochem.8b00994 ◽

2018 ◽

Vol 58 (3) ◽

pp. 166-170 ◽

Cited By ~ 10

Author(s):

Bhanu Pratap Singh Chouhan ◽

Shayida Maimaiti ◽

Madhuri Gade ◽

Paola Laurino

Keyword(s):

Rossmann Fold

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Is RNA Binding in the Rossmann Fold Essential for GAPDH Intranuclear Functions?

American Journal of Biochemistry and Biotechnology ◽

10.3844/ajbbsp.2016.86.94 ◽

2016 ◽

Vol 12 (2) ◽

pp. 86-94

Author(s):

Natalia Krynetskaia ◽

Manali Phadke ◽

Evgeny Krynetskiy

Keyword(s):

Rna Binding ◽

Rossmann Fold

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An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors

PLoS Biology ◽

10.1371/journal.pbio.1002396 ◽

2016 ◽

Vol 14 (3) ◽

pp. e1002396 ◽

Cited By ~ 43

Author(s):

Paola Laurino ◽

Ágnes Tóth-Petróczy ◽

Rubén Meana-Pañeda ◽

Wei Lin ◽

Donald G. Truhlar ◽

...

Keyword(s):

Common Ancestry ◽

Rossmann Fold ◽

The Common

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Secondary structure of NADPH: protochlorophyllide oxidoreductase examined by circular dichroism and prediction methods*

Biochemical Journal ◽

10.1042/bj3170549 ◽

1996 ◽

Vol 317 (2) ◽

pp. 549-555 ◽

Cited By ~ 28

Author(s):

Simon J. BIRVE ◽

Eva SELSTAM ◽

Lennart B.-Å. JOHANSSON

Keyword(s):

Secondary Structure ◽

Fluorescence Emission ◽

Random Coil ◽

Prolamellar Body ◽

Interfacial Region ◽

Protochlorophyllide Oxidoreductase ◽

Loop Region ◽

Rossmann Fold ◽

Α Helix ◽

Β Sheet

To study the secondary structure of the enzyme NADPH: protochlorophyllide oxidoreductase (PCOR), a novel method of enzyme isolation was developed. The detergent isotridecyl poly(ethylene glycol) ether (Genapol X-080) selectively solubilizes the enzyme from a prolamellar-body fraction isolated from wheat (Triticum aestivumL.). The solubilized fraction was further purified by ion-exchange chromatography. The isolated enzyme was studied by fluorescence spectroscopy at 77 K, and by CD spectroscopy. The fluorescence-emission spectra revealed that the binding properties of the substrate and co-substrate were preserved and that photo-reduction occurred. The CD spectra of PCOR were analysed for the relative amounts of the secondary structures, α-helix, β-sheet, turn and random coil. The secondary-structure composition was estimated to be 33% α-helix, 19% β-sheet, 20% turn and 28% random coil. These values are in agreement with those predicted by the Predict Heidelberg Deutschland and self-optimized prediction method from alignments methods. The enzyme has some amino acid identity with other NADPH-binding enzymes containing the Rossmann fold. The Rossmann-fold fingerprint motif is localized in the N-terminal region and at the expected positions in the predicted secondary structure. It is suggested that PCOR is anchored to the interfacial region of the membrane by either a β-sheet or an α-helical region containing tryptophan residues. A hydrophobic loop-region could also be involved in membrane anchoring.

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