Crystal structures of the editing domain of <i>Escherichia coli</i> leucyl-tRNA synthetase and its complexes with Met and Ile reveal a lock-and-key mechanism for amino acid discrimination

Yun-qing, Liu; Liao, Jing; Zhu, Bin; Wang, En‐Duo; Ding, Jianping

doi:10.1042/bj20051249

Cited by 32 publications

(27 citation statements)

References 34 publications

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“…The CP1 domain of LeuRS contains a threonine-rich region that comprises a portion of the editing active site (13,15,31,33,46). A second downstream region is marked by a universally conserved aspartic acid that forms a hydrogen bond with the amino moiety of the bound amino acid (Fig.…”

Section: Yeast Mitochondrial Leurs Is Active In Post-transfer Editing-mentioning

confidence: 99%

A Viable Amino Acid Editing Activity in the Leucyl-tRNA Synthetase CP1-splicing Domain Is Not Required in the Yeast Mitochondria

Karkhanis

Boniecki

Poruri

et al. 2006

Journal of Biological Chemistry

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Aminoacyl-tRNA synthetases are a family of enzymes that are responsible for translating the genetic code in the first step of protein synthesis. Some aminoacyl-tRNA synthetases have editing activities to clear their mistakes and enhance fidelity. Leucyl-tRNA synthetases have a hydrolytic active site that resides in a discrete amino acid editing domain called CP1. Mutational analysis within yeast mitochondrial leucyl-tRNA synthetase showed that the enzyme has maintained an editing active site that is competent for post-transfer editing of mischarged tRNA similar to other leucyl-tRNA synthetases. These mutations that altered or abolished leucyl-tRNA synthetase editing were introduced into complementation assays. Cell viability and mitochondrial function were largely unaffected in the presence of high levels of non-leucine amino acids. In contrast, these editing-defective mutations limited cell viability in Escherichia coli. It is possible that the yeast mitochondria have evolved to tolerate lower levels of fidelity in protein synthesis or have developed alternate mechanisms to enhance discrimination of leucine from non-cognate amino acids that can be misactivated by leucyl-tRNA synthetase.

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Section: Yeast Mitochondrial Leurs Is Active In Post-transfer Editing-mentioning

confidence: 99%

A Viable Amino Acid Editing Activity in the Leucyl-tRNA Synthetase CP1-splicing Domain Is Not Required in the Yeast Mitochondria

Karkhanis

Boniecki

Poruri

et al. 2006

Journal of Biological Chemistry

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“…A large ensemble of LeuRS co-crystal structures that include tRNA complexes in the aminoacylation and editing conformation have failed to suggest a specific role for the LSdomain (5,9,(13)(14)(15)(16). The co-crystal structure of P. horikoshii LeuRS with the tRNA in the aminoacylation conformation has been solved (13).…”

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confidence: 99%

A Unique Insert of Leucyl-tRNA Synthetase Is Required for Aminoacylation and Not Amino Acid Editing

Martinis

2007

Biochemistry

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Leucyl-tRNA synthetase (LeuRS) is a class I enzyme, which houses its aminoacylation active site in a canonical core that is defined by a Rossmann nucleotide binding fold. In addition, many LeuRSs bear a unique polypeptide insert comprised of about 50 amino acids located just upstream of the conserved KMSKS sequence. The role of this leucine-specific domain (LS-domain) remains undefined. We hypothesized that this domain may be important for substrate recognition in aminoacylation and/or amino acid editing. We carried out a series of deletion mutations and chimeric swaps within the leucine-specific domain of Escherichia coli. Our results support that the leucinespecific domain is critical for aminoacylation, but not required for editing activity. Kinetic analysis determined that deletion of the LS-domain primarily impacts k cat . Because of its proximity to the aminoacylation active site, we propose that this domain interacts with the tRNA during amino acid activation and/or tRNA aminoacylation. Although the leucine-specific domain does not appear to be important to the editing complex, it remains possible that it aids the dynamic translocation process that moves tRNA from the aminoacylation to the editing complex.Aminoacylation is catalyzed by an ancient family of enzymes called the aminoacyl-tRNA synthetases (aaRS) (1,2). It is important to translation that the aaRS correctly link amino acid to the corresponding tRNA acceptors. Each of the aaRS is responsible for covalently attaching one of twenty standard amino acids to a set of cognate tRNA isoacceptors. The esterification of amino acid to tRNA occurs via a two-step reaction:The first reversible step involves the activation of an amino acid concomitant with ATP hydrolysis to form an aminoacyl-adenylate intermediate. The amino acid is then transferred from the adenylate intermediate to the 3′ terminal adenosine moiety of the tRNA. The charged aminoacyl-tRNA binds to EF-Tu and is transported to the ribosome to extend the polypeptide chain.Leucyl-tRNA synthetase (LeuRS) is a class I aaRS, and is responsible for accurately aminoacylating leucine to its cognate tRNA Leu isoacceptors (3). As is characteristic of all class I synthetases, the catalytic core is defined by a Rossmann nucleotide binding fold (4) that comprises the main body of the enzyme (5). This canonical class I core of LeuRS contains inserts and appendages (5-7). For example, the enzyme has an amino acid editing function that † This work was supported by the National Institutes of Health (GM63789). resides within a large insert called the connective polypeptide 1 (CP1) (8). In addition, a novel C-terminal domain has been proposed to be important for tRNA interactions (9-12).One unique small insert called the leucine-specific domain (LS-domain) is found in many bacterial LeuRSs (5). Its function remains undefined. This compact domain that is comprised of five β-strands and two short α-helices flanks the entrance of the aminoacylation active site (5). The LS-domain is inserted after the last β-...

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“…Recently we observed the same structural features in the newly reported X-ray structure of E. coli LeuRS CP1 domain. 26 Although our idea was proved to make sense though the currently available six structures, we hope that more 3D structures of class Ia aaRSs are reported so that the idea can be confirmed in near future. Amino acid binding mode in editing site and the role of each subunit.…”

Section: Resultsmentioning

confidence: 99%

Three Common Subunits in Editing Domains of Class Ia tRNA Synthetases

Lee¹,

Kwon²,

Briggs³

2007

Bulletin of the Korean Chemical Society

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To identify structural or functional common subunit(s) in the CP1 (editing) domains of class Ia tRNA synthetases, five available structures were compared and analyzed. Through the sequence alignments and structural overlapping of the CP1 domains, three conserved regions were identified near the amino acid binding site in the editing domain. Structural overlapping of the three subunits clearly showed the existence of three common structural subunits in all of the five editing RS structures. Based on the established experimental results and our modeling results, it is proposed that subunits 1 and 3 accommodate the incoming amino acid binding, while subunit 2 contributes to the interactions with the adenosine ring of the A76 to stabilize the overall tRNA binding. Since these subunits are critical for the editing reaction, we expect that these key structures should be conserved through the most class Ia editing RSs.

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Crystal structures of the editing domain of Escherichia coli leucyl-tRNA synthetase and its complexes with Met and Ile reveal a lock-and-key mechanism for amino acid discrimination

Cited by 32 publications

References 34 publications

A Viable Amino Acid Editing Activity in the Leucyl-tRNA Synthetase CP1-splicing Domain Is Not Required in the Yeast Mitochondria

A Viable Amino Acid Editing Activity in the Leucyl-tRNA Synthetase CP1-splicing Domain Is Not Required in the Yeast Mitochondria

A Unique Insert of Leucyl-tRNA Synthetase Is Required for Aminoacylation and Not Amino Acid Editing

Three Common Subunits in Editing Domains of Class Ia tRNA Synthetases

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