The Procapsid Binding Domain of φ29 Packaging RNA Has a Modular Architecture and Requires 2‘-Hydroxyl Groups in Packaging RNA Interaction†

Biochemistry ◽  
2005 ◽  
Vol 44 (26) ◽  
pp. 9348-9358 ◽  
Author(s):  
Yun Fang ◽  
Qi Cai ◽  
Peter Z. Qin
Keyword(s):  
Binding Domain ◽  
Hydroxyl Groups ◽  
Modular Architecture ◽  
Packaging Rna ◽  
Rna Interaction

scholarly journals The PUMILIO−RNA Interaction:  A Single RNA-Binding Domain Monomer Recognizes a Bipartite Target Sequence†

Biochemistry ◽  
1999 ◽  
Vol 38 (2) ◽  
pp. 596-604 ◽  
Author(s):  
Phillip D. Zamore ◽  
David P. Bartel ◽  
Ruth Lehmann ◽  
James R. Williamson
Keyword(s):  
Rna Binding ◽  
Binding Domain ◽  
Target Sequence ◽  
Rna Binding Domain ◽  
Rna Interaction

scholarly journals Effects of Mutations in the Substrate-Binding Domain of Poly[(R)-3-Hydroxybutyrate] (PHB) Depolymerase from Ralstonia pickettii T1 on PHB Degradation

2006 ◽  
Vol 72 (11) ◽  
pp. 7331-7338 ◽  
Author(s):  
Tomohiro Hiraishi ◽  
Yoko Hirahara ◽  
Yoshiharu Doi ◽  
Mizuo Maeda ◽  
Seiichi Taguchi
Keyword(s):  
High Frequency ◽  
High Throughput Screening ◽  
Substrate Binding ◽  
Random Mutagenesis ◽  
Hydrolytic Activity ◽  
Binding Domain ◽  
Hydroxyl Groups ◽  
Phb Depolymerase ◽  
Ralstonia Pickettii ◽  
Substrate Binding Domain

ABSTRACT Poly[(R)-3-hydroxybutyrate] (PHB) depolymerase from Ralstonia pickettii T1 (PhaZRpiT1) adsorbs to denatured PHB (dPHB) via its substrate-binding domain (SBD) to enhance dPHB degradation. To evaluate the amino acid residues participating in dPHB adsorption, PhaZRpiT1 was subjected to a high-throughput screening system consisting of PCR-mediated random mutagenesis targeted to the SBD gene and a plate assay to estimate the effects of mutations in the SBD on dPHB degradation by PhaZRpiT1. Genetic analysis of the isolated mutants with lowered activity showed that Ser, Tyr, Val, Ala, and Leu residues in the SBD were replaced by other residues at high frequency. Some of the mutant enzymes, which contained the residues replaced at high frequency, were applied to assays of dPHB degradation and adsorption, revealing that those residues are essential for full activity of both dPHB degradation and adsorption. These results suggested that PhaZRpiT1 adsorbs on the surface of dPHB not only via hydrogen bonds between hydroxyl groups of Ser in the enzyme and carbonyl groups in the PHB polymer but also via hydrophobic interaction between hydrophobic residues in the enzyme and methyl groups in the PHB polymer. The L441H enzyme, which displayed lower dPHB degradation and adsorption abilities, was purified and applied to a dPHB degradation assay to compare it with the wild-type enzyme. The kinetic analysis of the dPHB degradation suggested that lowering the affinity of the SBD towards dPHB causes a decrease in the dPHB degradation rate without the loss of its hydrolytic activity for the polymer chain.

scholarly journals LOTUS domain is a novel class of G-rich and G-quadruplex RNA binding domain

2020 ◽  
Vol 48 (16) ◽  
pp. 9262-9272 ◽  
Author(s):  
Deqiang Ding ◽  
Chao Wei ◽  
Kunzhe Dong ◽  
Jiali Liu ◽  
Alexander Stanton ◽  
...  
Keyword(s):  
Rna Binding ◽  
Specific Interaction ◽  
Binding Activity ◽  
Binding Domain ◽  
Binding Property ◽  
Domain Family ◽  
Rna Sequences ◽  
G Quadruplex ◽  
Rna Binding Domain ◽  
Rna Interaction

Abstract LOTUS domains are helix-turn-helix protein folds identified in essential germline proteins and are conserved in prokaryotes and eukaryotes. Despite originally predicted as an RNA binding domain, its molecular binding activity towards RNA and protein is controversial. In particular, the most conserved binding property for the LOTUS domain family remains unknown. Here, we uncovered an unexpected specific interaction of LOTUS domains with G-rich RNA sequences. Intriguingly, LOTUS domains exhibit high affinity to RNA G-quadruplex tertiary structures implicated in diverse cellular processes including piRNA biogenesis. This novel LOTUS domain-RNA interaction is conserved in bacteria, plants and animals, comprising the most ancient binding feature of the LOTUS domain family. By contrast, LOTUS domains do not preferentially interact with DNA G-quadruplexes. We further show that a subset of LOTUS domains display both RNA and protein binding activities. These findings identify the LOTUS domain as a specialized RNA binding domain across phyla and underscore the molecular mechanism underlying the function of LOTUS domain-containing proteins in RNA metabolism and regulation.

scholarly journals Selection of a novel class of RNA–RNA interaction motifs based on the ligase ribozyme with defined modular architecture

2008 ◽  
Vol 36 (11) ◽  
pp. 3600-3607 ◽  
Author(s):  
Shoji P. Ohuchi ◽  
Yoshiya Ikawa ◽  
Yoshikazu Nakamura
Keyword(s):  
Modular Architecture ◽  
Rna Interaction ◽  
Selection Of

scholarly journals RNA Binding Domain of Telomerase Reverse Transcriptase

2001 ◽  
Vol 21 (4) ◽  
pp. 990-1000 ◽  
Author(s):  
Cary K. Lai ◽  
James R. Mitchell ◽  
Kathleen Collins
Keyword(s):  
Catalytic Activity ◽  
Reverse Transcriptase ◽  
Rna Binding ◽  
Binding Domain ◽  
Amino Terminus ◽  
Telomerase Reverse Transcriptase ◽  
Telomerase Rna ◽  
Sequence Motifs ◽  
Rna Binding Domain ◽  
Rna Interaction

ABSTRACT Telomerase is a ribonucleoprotein reverse transcriptase that extends the ends of chromosomes. The two telomerase subunits essential for catalysis in vitro are the telomerase reverse transcriptase (TERT) and the telomerase RNA. Using truncations and site-specific mutations, we identified sequence elements of TERT and telomerase RNA required for catalytic activity and protein-RNA interaction for Tetrahymena thermophila telomerase. We found that the TERT amino and carboxyl termini, although evolutionarily poorly conserved, are nonetheless important for catalytic activity. In contrast, high-affinity telomerase RNA binding requires only a small region in the amino terminus of TERT. Surprisingly, the TERT region necessary and sufficient for telomerase RNA binding is completely separable from the reverse transcriptase motifs. The minimalTetrahymena TERT RNA binding domain contains two sequence motifs with ciliate-specific conservation and one TERT motif with conservation across all species. With human TERT, we demonstrate that a similar region within the TERT amino terminus is essential for human telomerase RNA binding as well. Finally, we defined theTetrahymena telomerase RNA sequences that are essential for TERT interaction. We found that a four-nucleotide region 5′ of the template is critical for TERT binding and that the 5′ end of telomerase RNA is sufficient for TERT binding. Our results reveal at least one evolutionarily conserved molecular mechanism by which the telomerase reverse transcriptase is functionally specialized for obligate use of an internal RNA template.

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