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Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex.

Kim KR, Park SH, Kim HS, Rhee KH, Kim BG, Kim DG, Park MS, Kim HJ, Kim S, Han BW - Proteins (2013)

Bottom Line: Human cytosolic aspartyl-tRNA synthetase (DRS) catalyzes the attachment of the amino acid aspartic acid to its cognate tRNA and it is a component of the multi-tRNA synthetase complex (MSC) which has been known to be involved in unexpected signaling pathways.DRS is a homodimer with a dimer interface of 3750.5 Å(2) which comprises 16.6% of the monomeric surface area.Our structure reveals the C-terminal end of the N-helix which is considered as a unique addition in DRS, and its conformation further supports the switching model of the N-helix for the transfer of tRNA(Asp) to elongation factor 1α.

View Article: PubMed Central - PubMed

Affiliation: Research Institute of Pharmaceutical Sciences, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, 151-742, Korea.

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N-terminal extension, PTM, and key intermolecular interaction of DRS. (A) The switching model of the N-helix with our DRS structure. (B) PTM analyses. Acetylation, phosphorylation, and ubiquitination sites are shown as blue, red, and yellow circles, respectively. PTM sites uniquely observed in this study and residues observed both in the database and in our study are surrounded by black boxes and dotted boxes, respectively. Ser146, which is expected to play a key role in the organization of DRS, is marked with a red asterisk. (C) Sequence alignment of the interface residues of anticodon-binding domain and catalytic domain of DRSs from various organisms. Ser146, Gly462, and Ala463 of human DRS are marked with red asterisks. (D) Close-up view of Ser146 and the intermolecular interaction of DRS dimer. The structure of human DRS is superimposed with that of human KRS shown in a gray cartoon model.
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fig02: N-terminal extension, PTM, and key intermolecular interaction of DRS. (A) The switching model of the N-helix with our DRS structure. (B) PTM analyses. Acetylation, phosphorylation, and ubiquitination sites are shown as blue, red, and yellow circles, respectively. PTM sites uniquely observed in this study and residues observed both in the database and in our study are surrounded by black boxes and dotted boxes, respectively. Ser146, which is expected to play a key role in the organization of DRS, is marked with a red asterisk. (C) Sequence alignment of the interface residues of anticodon-binding domain and catalytic domain of DRSs from various organisms. Ser146, Gly462, and Ala463 of human DRS are marked with red asterisks. (D) Close-up view of Ser146 and the intermolecular interaction of DRS dimer. The structure of human DRS is superimposed with that of human KRS shown in a gray cartoon model.

Mentions: In higher eukaryotes, additional domains or motifs in a specific AARS result in new functions. In the case of DRS, KRS, and NRS, they contain the N-helix that is named after the helical conformation in part of their N-terminal extension region.11,23 The previously determined NMR structure of the N-terminal extension of DRS revealed the conformational flexibility caused by the β-turn followed by one α-helix and the N-terminal extension plays a crucial role in the interaction between tRNAAsp and EF-1α.12–14 In our crystal structure, the C-terminal end of the α-helix in the N-terminal extension was observed, comprising Lys26, Glu27, and Arg28 although the N-terminal region was less-ordered. To get a glimpse of the whole N-helix structure, we superposed the structurally well-resolved C-terminal end of the N-terminal extension residue Glu27 and Arg28 with the α-helix of the NMR structure, considering the helical wheel conformation (Supporting Information Fig. S2). The α-helix in the N-terminal extension is amphipathic and the hydrophilic face of the amphipathic helix could interact with positively charged residues Arg8 and Lys9 in the N-terminus by the conformational change on the flexible β-turn.14 Our crystal structure further supports the structural switching model of the N-terminal extension of DRS in the aid of the direct transfer of tRNAAsp to EF-1α [Fig. 2(A)].


Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex.

Kim KR, Park SH, Kim HS, Rhee KH, Kim BG, Kim DG, Park MS, Kim HJ, Kim S, Han BW - Proteins (2013)

N-terminal extension, PTM, and key intermolecular interaction of DRS. (A) The switching model of the N-helix with our DRS structure. (B) PTM analyses. Acetylation, phosphorylation, and ubiquitination sites are shown as blue, red, and yellow circles, respectively. PTM sites uniquely observed in this study and residues observed both in the database and in our study are surrounded by black boxes and dotted boxes, respectively. Ser146, which is expected to play a key role in the organization of DRS, is marked with a red asterisk. (C) Sequence alignment of the interface residues of anticodon-binding domain and catalytic domain of DRSs from various organisms. Ser146, Gly462, and Ala463 of human DRS are marked with red asterisks. (D) Close-up view of Ser146 and the intermolecular interaction of DRS dimer. The structure of human DRS is superimposed with that of human KRS shown in a gray cartoon model.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3824080&req=5

fig02: N-terminal extension, PTM, and key intermolecular interaction of DRS. (A) The switching model of the N-helix with our DRS structure. (B) PTM analyses. Acetylation, phosphorylation, and ubiquitination sites are shown as blue, red, and yellow circles, respectively. PTM sites uniquely observed in this study and residues observed both in the database and in our study are surrounded by black boxes and dotted boxes, respectively. Ser146, which is expected to play a key role in the organization of DRS, is marked with a red asterisk. (C) Sequence alignment of the interface residues of anticodon-binding domain and catalytic domain of DRSs from various organisms. Ser146, Gly462, and Ala463 of human DRS are marked with red asterisks. (D) Close-up view of Ser146 and the intermolecular interaction of DRS dimer. The structure of human DRS is superimposed with that of human KRS shown in a gray cartoon model.
Mentions: In higher eukaryotes, additional domains or motifs in a specific AARS result in new functions. In the case of DRS, KRS, and NRS, they contain the N-helix that is named after the helical conformation in part of their N-terminal extension region.11,23 The previously determined NMR structure of the N-terminal extension of DRS revealed the conformational flexibility caused by the β-turn followed by one α-helix and the N-terminal extension plays a crucial role in the interaction between tRNAAsp and EF-1α.12–14 In our crystal structure, the C-terminal end of the α-helix in the N-terminal extension was observed, comprising Lys26, Glu27, and Arg28 although the N-terminal region was less-ordered. To get a glimpse of the whole N-helix structure, we superposed the structurally well-resolved C-terminal end of the N-terminal extension residue Glu27 and Arg28 with the α-helix of the NMR structure, considering the helical wheel conformation (Supporting Information Fig. S2). The α-helix in the N-terminal extension is amphipathic and the hydrophilic face of the amphipathic helix could interact with positively charged residues Arg8 and Lys9 in the N-terminus by the conformational change on the flexible β-turn.14 Our crystal structure further supports the structural switching model of the N-terminal extension of DRS in the aid of the direct transfer of tRNAAsp to EF-1α [Fig. 2(A)].

Bottom Line: Human cytosolic aspartyl-tRNA synthetase (DRS) catalyzes the attachment of the amino acid aspartic acid to its cognate tRNA and it is a component of the multi-tRNA synthetase complex (MSC) which has been known to be involved in unexpected signaling pathways.DRS is a homodimer with a dimer interface of 3750.5 Å(2) which comprises 16.6% of the monomeric surface area.Our structure reveals the C-terminal end of the N-helix which is considered as a unique addition in DRS, and its conformation further supports the switching model of the N-helix for the transfer of tRNA(Asp) to elongation factor 1α.

View Article: PubMed Central - PubMed

Affiliation: Research Institute of Pharmaceutical Sciences, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, 151-742, Korea.

Show MeSH
Related in: MedlinePlus