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Homology model of the human tRNA splicing ligase RtcB
Author(s) -
Nandy Argha,
SaenzMéndez Patricia,
Gorman Adrienne M.,
Samali Afshin,
Eriksson Leif A.
Publication year - 2017
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25352
Subject(s) - active site , dna ligase , chemistry , protein data bank (rcsb pdb) , homology modeling , binding site , biochemistry , ubiquitin ligase , rna splicing , stereochemistry , enzyme , rna , ubiquitin , gene
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 ( h RtcB) in complex with manganese and covalently bound GMP built from the Pyrococcus horikoshii RtcB ( b RtcB) crystal structure, PDB ID 4DWQA. The structure is analyzed in terms of stereochemical quality, folding reliability, secondary structure similarity with b RtcB, druggability of the active site binding pocket and its metal‐binding microenvironment. In comparison with b RtcB, loss of a manganese‐coordinating water and movement of Asn226 (Asn202 in 4DWQA) to form metal‐ligand coordination, demonstrates the uniqueness of the h 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.