Tomoyuki Numata
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View article: Cryo-EM structure of Archaeoglobus fulgidus type III-B CRISPR-Cas effector and intermediate crRNA processing during effector assembly
Cryo-EM structure of Archaeoglobus fulgidus type III-B CRISPR-Cas effector and intermediate crRNA processing during effector assembly Open
Type III CRISPR-Cas effectors recognize target RNAs complementary to the crRNA guide, activating diverse downstream antiviral responses. In contrast to type III-A systems, the architecture of the type III-B effector (Cmr), comprising six p…
View article: Msp1 and Pex19‐Pex3 cooperate to achieve correct localization of Pex15 to peroxisomes
Msp1 and Pex19‐Pex3 cooperate to achieve correct localization of Pex15 to peroxisomes Open
Yeast Msp1 is a dual‐localized AAA‐ATPase on the mitochondrial outer membrane (OM) and peroxisomal membrane. We previously showed that Msp1 transfers mistargeted tail‐anchored (TA) proteins from mitochondria to the endoplasmic reticulum (E…
View article: Msp1 and Pex19-Pex3 cooperate to achieve correct localization of Pex15 to peroxisomes
Msp1 and Pex19-Pex3 cooperate to achieve correct localization of Pex15 to peroxisomes Open
Yeast Msp1 is a dual-localized AAA-ATPase on the mitochondrial outer membrane (OM) and peroxisomal membrane. We previously showed that Msp1 transfers mistargeted tail-anchored (TA) proteins from mitochondria to the endoplasmic reticulum (E…
View article: Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression
Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression Open
Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands …
View article: Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression
Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression Open
Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands …
View article: Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression
Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression Open
Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands …
View article: GET pathway mediates transfer of mislocalized tail-anchored proteins from mitochondria to the ER
GET pathway mediates transfer of mislocalized tail-anchored proteins from mitochondria to the ER Open
Tail-anchored (TA) membrane proteins have a potential risk to be mistargeted to the mitochondrial outer membrane (OM). Such mislocalized TA proteins can be extracted by the mitochondrial AAA-ATPase Msp1 from the OM and transferred to the E…
View article: Genetic and Biochemical Characterizations of aLhr1 Helicase in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius
Genetic and Biochemical Characterizations of aLhr1 Helicase in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius Open
Homologous recombination (HR) refers to the process of information exchange between homologous DNA duplexes and is composed of four main steps: end resection, strand invasion and formation of a Holliday junction (HJ), branch migration, and…
View article: A conserved loop structure of GH19 chitinases assists the enzyme function from behind the core-functional region
A conserved loop structure of GH19 chitinases assists the enzyme function from behind the core-functional region Open
Plant GH19 chitinases have several loop structures, which may define their enzymatic properties. Among these loops, the longest loop, Loop-III, is most frequently conserved in GH19 enzymes. A GH19 chitinase from the moss Bryum coronatum (B…
View article: Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome
Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome Open
Genomic DNA replication requires replisome assembly. We show here the molecular mechanism by which CMG (GAN–MCM–GINS)-like helicase cooperates with the family D DNA polymerase (PolD) in Thermococcus kodakarensis. The archaeal GINS contains…
View article: DNA polymerase D temporarily connects primase to the CMG-like helicase before interacting with proliferating cell nuclear antigen
DNA polymerase D temporarily connects primase to the CMG-like helicase before interacting with proliferating cell nuclear antigen Open
The eukaryotic replisome is comprised of three family-B DNA polymerases (Polα, δ and ϵ). Polα forms a stable complex with primase to synthesize short RNA-DNA primers, which are subsequently elongated by Polδ and Polϵ in concert with prolif…
View article: A Chemical Probe Based on the PreQ1 Metabolite Enables Transcriptome-wide Mapping of Binding Sites
A Chemical Probe Based on the PreQ1 Metabolite Enables Transcriptome-wide Mapping of Binding Sites Open
The role of metabolite-responsive riboswitches in regulating gene expression in bacteria is well known and makes them useful systems for the study of RNA-small molecule interactions. Here, we study the PreQ1 riboswitch system, assessing si…
View article: Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease
Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease Open
Modified uridine containing taurine, 5-taurinomethyluridine (τm(5)U), is found at the anticodon first position of mitochondrial (mt-)transfer RNAs (tRNAs). Previously, we reported that τm(5)U is absent in mt-tRNAs with pathogenic mutations…
View article: Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a <i>Paenibacillus</i> sp. IK-5 chitosanase/glucanase
Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a <i>Paenibacillus</i> sp. IK-5 chitosanase/glucanase Open
An antifungal chitosanase/glucanase isolated from the soil bacterium Paenibacillus sp. IK-5 has two CBM32 chitosan-binding modules (DD1 and DD2) linked in tandem at the C-terminus. In order to obtain insights into the mechanism of chitosan…
View article: [Review: Symposium on Applied Glycoscience] Interaction of Chitosan-binding Modules with Chitosan as Revealed by NMR and X-Ray Crystallography
[Review: Symposium on Applied Glycoscience] Interaction of Chitosan-binding Modules with Chitosan as Revealed by NMR and X-Ray Crystallography Open
土壌細菌の一種であるPaenibacillus sp. IK5は，触媒モジュール (GH8) とフィブロネクチンタイプIIIモジュール，2 つの糖質結合モジュール(CBM32) からなるモジュラー型キトサナーゼを産生することが知られている．NMRおよび等温滴定型熱量計によるキトサンオリゴ糖の結合実験の結果，これら2 つのCBM32 (DD1およびDD2) は，高いアミノ酸配列相同性をもつにもかかわらず，キトサンオリゴ糖に対して異なる結合性を示すことがわかった．この結合性の違…
View article: CCDC 1452936: Experimental Crystal Structure Determination
CCDC 1452936: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …