Crystal Structure of Human Seryl-tRNA Synthetase and Ser-SA Complex Reveals a Molecular Lever Specific to Higher Eukaryotes Xiaoling Xu, Yi Shi, Xiang-Lei.

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Presentation transcript:

Crystal Structure of Human Seryl-tRNA Synthetase and Ser-SA Complex Reveals a Molecular Lever Specific to Higher Eukaryotes Xiaoling Xu, Yi Shi, Xiang-Lei Yang Structure Volume 21, Issue 11, Pages 2078-2086 (November 2013) DOI: 10.1016/j.str.2013.08.021 Copyright © 2013 Elsevier Ltd Terms and Conditions

Structure 2013 21, 2078-2086DOI: (10.1016/j.str.2013.08.021) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 1 Overall Structure of Human SerRS in Complex with Ser-SA and the Conformational Change of TBD (A) Crystal structure of human SerRS bound with Ser-SA. The secondary structure elements are labeled. Inset: Structure of the dimeric SerRS with the second subunit generated by crystallographic symmetry operation shown in gray. (B) Ser-SA induced conformational change of the TBD is specific to human SerRS. The Ser-SA bound and free structures from human (PDB IDs 4L87 and 3VBB), C. albicans (PDB IDs 3QO8 and 3QNE), T. brucei (PDB IDs 3LSS and 3LSQ), P. horikoshii (PDB IDs 2DQ0 and 2ZR3), and T. thermophilus (PDB IDs 1SET and 1SRY) are superimposed at the AD. Free SerRSs are shown in gray and the Ser-SA bound SerRSs in colors. See also Figures S1–S3. Structure 2013 21, 2078-2086DOI: (10.1016/j.str.2013.08.021) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 2 Ser-SA-Induced Conformational Change in Human SerRS Is Caused by Shifting the TBD-AD Interactions from α13 in Lower Organisms to α9–α10 in Human SerRS The hydrogen bonding interactions in the “hinge” region mediating TBD (yellow) and AD (green) in crystal structures of (A) human SerRS bound with Ser-SA (PDB ID 4L87), (B) ligand-free human SerRS (PDB ID 3VBB), (C) C. albicans SerRS bound with Ser-SA (PDB ID 3QO8), (D) T. brucei SerRS bound with ATP (PDB ID 3LSS), (E) P. horikoshii SerRS bound with Ser-SA (PDB ID 2DQ0), and (F) T. thermophiles SerRS bound with Ser-SA (PDB ID 1SET). The secondary structures are labeled in gray. See also Figures S4 and S5. Structure 2013 21, 2078-2086DOI: (10.1016/j.str.2013.08.021) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 3 Conservations of Key Residues Involved in the TBD-AD Interaction and of the Insertions I and II in Higher Eukaryotes Key residues involved in communication of TBD and AD are highlighted in yellow (TBD) or in green (AD). The vertebrate-specific Insertions I and II are shown in salmon. Structure 2013 21, 2078-2086DOI: (10.1016/j.str.2013.08.021) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 4 Structural and Functional Analyses of Insertions I and II (A) Leucine-rich motif of Insertion I (salmon) forms extensive hydrophobic interactions with residues from α3 and α5 (yellow). (B) Structural environment of Insertion II (salmon) near the dimer interface and the active site. (C) Aminoacylation assay indicating that deletion of Insertion I has a larger effect on SerRS aminoacylation activity than deletion of Insertion II. (D) ATP-PPi exchange assay confirming the effect of Insertion I on the active site. Structure 2013 21, 2078-2086DOI: (10.1016/j.str.2013.08.021) Copyright © 2013 Elsevier Ltd Terms and Conditions