Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD. (Q30660836)

11 August 2017

Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD. (English)

1 reference

11 August 2017

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

Isao Masuda

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

Shun-ichi Sekine

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

Ya-Ming Hou

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

Shigeyuki Yokoyama

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

6

Se Won Suh

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

author name string

Ken-ichi Yoshida

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

Sakurako Goto-Ito

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

language of work or name

English

0 references

publication date

16 July 2015

1 reference

Proceedings of the National Academy of Sciences of the United States of America

11 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

volume

112

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

page(s)

E4197-205

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

issue

31

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

A divalent metal ion-dependent N(1)-methyl transfer to G37-tRNA.

14 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Physiological and Molecular Timing of the Glucose to Acetate Transition in Escherichia coli

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Selective inhibitors of bacterial t-RNA-(N(1)G37) methyltransferase (TrmD) that demonstrate novel ordering of the lid domain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Recognition of guanosine by dissimilar tRNA methyltransferases.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Differentiating analogous tRNA methyltransferases by fragments of the methyl donor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

The Bowen-Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Ψ1191 in yeast 18S rRNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Control of catalytic cycle by a pair of analogous tRNA modification enzymes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Features and development of Coot

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

PHENIX: a comprehensive Python-based system for macromolecular structure solution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Phasercrystallographic software

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Comparative genomic assessment of novel broad-spectrum targets for antibacterial drugs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Version 1.2 of the Crystallography and NMR system

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Insights into Catalysis by a Knotted TrmD tRNA Methyltransferase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

An enzyme with a deep trefoil knot for the active-site architecture

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Improvement of reading frame maintenance is a common function for several tRNA modifications

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

A primordial tRNA modification required for the evolution of life?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

ESPript: analysis of multiple sequence alignments in PostScript

20 June 2018

1 reference

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Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Functional analysis of the ffh-trmD region of the Escherichia coli chromosome by using reverse genetics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Bacterial peptide chain release factors: conserved primary structure and possible frameshift regulation of release factor 2.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Expression of peptide chain release factor 2 requires high-efficiency frameshift.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4534213

Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine.

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1422981112

Three modified nucleosides present in the anticodon stem and loop influence the in vivo aa-tRNA selection in a tRNA-dependent manner.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1422981112

A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1422981112

Distinct origins of tRNA(m1G37) methyltransferase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1422981112

NMRPipe: a multidimensional spectral processing system based on UNIX pipes

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1422981112

Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1422981112

Processing of X-ray diffraction data collected in oscillation mode

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26183229

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Chromosomal location and cloning of the gene (trmD) responsible for the synthesis of tRNA (m1G) methyltransferase in Escherichia coli K-12

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26183229

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1422981112

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26183229%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

1 reference