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Homology model of the human tRNA splicing ligase RtcB

Overview of attention for article published in Proteins: Structure, Function, and Bioinformatics, August 2017
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Title
Homology model of the human tRNA splicing ligase RtcB
Published in
Proteins: Structure, Function, and Bioinformatics, August 2017
DOI 10.1002/prot.25352
Pubmed ID
Authors

Argha Nandy, Patricia Saenz‐Méndez, Adrienne M. Gorman, Afshin Samali, Leif A. Eriksson

Abstract

RtcB is an essential human tRNA ligase required for ligating the 2',3'-cyclic phosphate and 5'-hydroxyl termini of cleaved tRNA halves during tRNA splicing and XBP1 fragments during endoplasmic reticulum stress. Activation of XBP1 has been implicated in various human tumors including breast cancer. Here we present, for the first time, a homology model of human RtcB (hRtcB) in complex with manganese and covalently bound GMP built from the Pyrococcus horikoshii RtcB (bRtcB) crystal structure, PDB ID 4DWQA. The structure is analyzed in terms of stereochemical quality, folding reliability, secondary structure similarity with bRtcB, druggability of the active site binding pocket and its metal-binding microenvironment. In comparison with bRtcB, loss of a manganese-coordinating water and movement of Asn226 (Asn202 in 4DWQA) to form metal-ligand coordination, demonstrates the uniqueness of the human RtcB model. Rotation of GMP leads to the formation of an additional metal-ligand coordination (Mn-O). Umbrella sampling simulations of Mn binding in wild type and the catalytically inactive C122A mutant reveal a clear reduction of Mn binding ability in the mutant, thus explaining the loss of activity therein. Our results furthermore clearly show that the GTP binding site of the enzyme is a well-defined pocket that can be utilized as target site for in silico drug discovery. This article is protected by copyright. All rights reserved.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 25 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 25 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 6 24%
Other 4 16%
Student > Master 3 12%
Professor > Associate Professor 3 12%
Student > Doctoral Student 2 8%
Other 4 16%
Unknown 3 12%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 9 36%
Agricultural and Biological Sciences 7 28%
Chemistry 4 16%
Pharmacology, Toxicology and Pharmaceutical Science 1 4%
Unknown 4 16%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 21 September 2017.
All research outputs
#16,725,651
of 25,382,440 outputs
Outputs from Proteins: Structure, Function, and Bioinformatics
#2,130
of 3,332 outputs
Outputs of similar age
#198,063
of 327,568 outputs
Outputs of similar age from Proteins: Structure, Function, and Bioinformatics
#16
of 27 outputs
Altmetric has tracked 25,382,440 research outputs across all sources so far. This one is in the 32nd percentile – i.e., 32% of other outputs scored the same or lower than it.
So far Altmetric has tracked 3,332 research outputs from this source. They receive a mean Attention Score of 3.6. This one is in the 33rd percentile – i.e., 33% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 327,568 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 36th percentile – i.e., 36% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 27 others from the same source and published within six weeks on either side of this one. This one is in the 37th percentile – i.e., 37% of its contemporaries scored the same or lower than it.