Structural Basis for Substrate Recognition by the Editing Domain of Isoleucyl-tRNA Synthetase

2006 ◽  
Vol 359 (4) ◽  
pp. 901-912 ◽  
Author(s):  
Ryuya Fukunaga ◽  
Shigeyuki Yokoyama
Keyword(s):  
Substrate Recognition ◽  
Trna Synthetase ◽  
Structural Basis ◽  
Editing Domain

scholarly journals Conformational and chemical selection by a trans-acting editing domain

2017 ◽  
Vol 114 (33) ◽  
pp. E6774-E6783 ◽  
Author(s):  
Eric M. Danhart ◽  
Marina Bakhtina ◽  
William A. Cantara ◽  
Alexandra B. Kuzmishin ◽  
Xiao Ma ◽  
...  
Keyword(s):  
Molecular Sieves ◽  
Caulobacter Crescentus ◽  
Nmr Relaxation ◽  
Trna Synthetase ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Computational Docking ◽  
Substrate Analogs ◽  
Editing Domain ◽  
Dynamics Simulations

Molecular sieves ensure proper pairing of tRNAs and amino acids during aminoacyl-tRNA biosynthesis, thereby avoiding detrimental effects of mistranslation on cell growth and viability. Mischarging errors are often corrected through the activity of specialized editing domains present in some aminoacyl-tRNA synthetases or via single-domain trans-editing proteins. ProXp-ala is a ubiquitous trans-editing enzyme that edits Ala-tRNAPro, the product of Ala mischarging by prolyl-tRNA synthetase, although the structural basis for discrimination between correctly charged Pro-tRNAPro and mischarged Ala-tRNAAla is unclear. Deacylation assays using substrate analogs reveal that size discrimination is only one component of selectivity. We used NMR spectroscopy and sequence conservation to guide extensive site-directed mutagenesis of Caulobacter crescentus ProXp-ala, along with binding and deacylation assays to map specificity determinants. Chemical shift perturbations induced by an uncharged tRNAPro acceptor stem mimic, microhelixPro, or a nonhydrolyzable mischarged Ala-microhelixPro substrate analog identified residues important for binding and deacylation. Backbone 15N NMR relaxation experiments revealed dynamics for a helix flanking the substrate binding site in free ProXp-ala, likely reflecting sampling of open and closed conformations. Dynamics persist on binding to the uncharged microhelix, but are attenuated when the stably mischarged analog is bound. Computational docking and molecular dynamics simulations provide structural context for these findings and predict a role for the substrate primary α-amine group in substrate recognition. Overall, our results illuminate strategies used by a trans-editing domain to ensure acceptance of only mischarged Ala-tRNAPro, including conformational selection by a dynamic helix, size-based exclusion, and optimal positioning of substrate chemical groups.

Structural Basis for Genetic-Code Expansion with Various Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase

2018 ◽  
Author(s):  
Tatsuo Yanagisawa ◽  
Mitsuo Kuratani ◽  
Eiko Seki ◽  
Nobumasa Hino ◽  
Kensaku Sakamoto ◽  
...  
Keyword(s):  
Genetic Code ◽  
Trna Synthetase ◽  
Structural Basis ◽  
Genetic Code Expansion

scholarly journals Structural Basis for Discrimination of L-Phenylalanine from L-Tyrosine by Phenylalanyl-tRNA Synthetase

Structure ◽  
2005 ◽  
Vol 13 (12) ◽  
pp. 1799-1807 ◽  
Author(s):  
Olga Kotik-Kogan ◽  
Nina Moor ◽  
Dmitry Tworowski ◽  
Mark Safro
Keyword(s):  
Trna Synthetase ◽  
Structural Basis

A naturally occurring nonapeptide functionally compensates for the CP1 domain of leucyl-tRNA synthetase to modulate aminoacylation activity

2012 ◽  
Vol 443 (2) ◽  
pp. 477-484 ◽  
Author(s):  
Min Tan ◽  
Wei Yan ◽  
Ru-Juan Liu ◽  
Meng Wang ◽  
Xin Chen ◽  
...  
Keyword(s):  
Catalytic Efficiency ◽  
Trna Synthetase ◽  
Modular Construction ◽  
Aquifex Aeolicus ◽  
Trna Synthetases ◽  
Naturally Occurring ◽  
Aminoacyl Trna Synthetases ◽  
Editing Domain ◽  
Editing Activity ◽  
Shed Light

aaRSs (aminoacyl-tRNA synthetases) establish the rules of the genetic code by catalysing the formation of aminoacyl-tRNA. The quality control for aminoacylation is achieved by editing activity, which is usually carried out by a discrete editing domain. For LeuRS (leucyl-tRNA synthetase), the CP1 (connective peptide 1) domain is the editing domain responsible for hydrolysing mischarged tRNA. The CP1 domain is universally present in LeuRSs, except MmLeuRS (Mycoplasma mobile LeuRS). The substitute of CP1 in MmLeuRS is a nonapeptide (MmLinker). In the present study, we show that the MmLinker, which is critical for the aminoacylation activity of MmLeuRS, could confer remarkable tRNA-charging activity on the inactive CP1-deleted LeuRS from Escherichia coli (EcLeuRS) and Aquifex aeolicus (AaLeuRS). Furthermore, CP1 from EcLeuRS could functionally compensate for the MmLinker and endow MmLeuRS with post-transfer editing capability. These investigations provide a mechanistic framework for the modular construction of aaRSs and their co-ordination to achieve catalytic efficiency and fidelity. These results also show that the pre-transfer editing function of LeuRS originates from its conserved synthetic domain and shed light on future study of the mechanism.

Crystal Structures of the Human and Fungal Cytosolic Leucyl-tRNA Synthetase Editing Domains: A Structural Basis for the Rational Design of Antifungal Benzoxaboroles

2009 ◽  
Vol 390 (2) ◽  
pp. 196-207 ◽  
Author(s):  
Elena Seiradake ◽  
Weimin Mao ◽  
Vincent Hernandez ◽  
Stephen J. Baker ◽  
Jacob J. Plattner ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Rational Design ◽  
Trna Synthetase ◽  
Structural Basis

Structural Basis of Furan-Amino Acid Recognition by a Polyspecific Aminoacyl-tRNA-Synthetase and its Genetic Encoding in Human Cells

ChemBioChem ◽  
2014 ◽  
Vol 15 (12) ◽  
pp. 1755-1760 ◽  
Author(s):  
Moritz J. Schmidt ◽  
Annemarie Weber ◽  
Moritz Pott ◽  
Wolfram Welte ◽  
Daniel Summerer
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Human Cells ◽  
Structural Basis ◽  
Aminoacyl Trna Synthetase ◽  
Genetic Encoding ◽  
Amino Acid Recognition

scholarly journals Structural Basis and Sequence Rules for Substrate Recognition by Tankyrase Explain the Basis for Cherubism Disease

Cell ◽  
2012 ◽  
Vol 148 (1-2) ◽  
pp. 376
Author(s):  
Sebastian Guettler ◽  
Jose LaRose ◽  
Evangelia Petsalaki ◽  
Gerald Gish ◽  
Andy Scotter ◽  
...  
Keyword(s):  
Substrate Recognition ◽  
Structural Basis ◽  
Sequence Rules

scholarly journals Structural basis of HMCES interactions with DNA reveals multivalent substrate recognition

2019 ◽  
Author(s):  
Levon Halabelian ◽  
Mani Ravichandran ◽  
Yanjun Li ◽  
Hong Zheng ◽  
L. Aravind ◽  
...  
Keyword(s):  
Dna Damage ◽  
Crystal Structures ◽  
Genome Instability ◽  
Substrate Recognition ◽  
Catalytic Triad ◽  
Structural Basis ◽  
Replication Forks ◽  
Abasic Sites ◽  
Stalled Replication Forks ◽  
Gapped Dna

ABSTRACTHMCES can covalently crosslink to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the HMCES SRAP domain in complex with DNA-damage substrates, revealing interactions with both single-stranded and duplex segments of 3’ overhang DNA. HMCES may also bind gapped DNA and 5’ overhang structures to align single stranded abasic sites for crosslinking to the conserved Cys2 of its catalytic triad.

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