4L87

Crystal structure of the human seryl-tRNA synthetase in complex with Ser-SA at 2.9 Angstrom resolution

Summary for 4L87

• Entry DOI: 10.2210/pdb4l87/pdb
• Related: 3VBB
• Descriptor: Serine--tRNA ligase, cytoplasmic, 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: long alpha-helices, seven-stranded anti-parallel beta-sheet, aminoacylation, trnaser, ligase
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm : P49591
• Total number of polymer chains: 1
• Total formula weight: 55094.23

Authors

Xu, X.,Yang, X.-L. (deposition date: 2013-06-16, release date: 2013-10-02, Last modification date: 2023-09-20)

Primary citation

Xu, X.,Shi, Y.,Yang, X.L.
Crystal Structure of Human Seryl-tRNA Synthetase and Ser-SA Complex Reveals a Molecular Lever Specific to Higher Eukaryotes.
Structure, 21:2078-2086, 2013

PubMed Abstract: Seryl-tRNA synthetase (SerRS), an essential enzyme for translation, also regulates vascular development. This "gain-of-function" has been linked to the UNE-S domain added to vertebrate SerRS during evolution. However, the significance of two insertions also specific to higher eukaryotic SerRS remains elusive. Here, we determined the crystal structure of human SerRS in complex with Ser-SA, an aminoacylation reaction intermediate analog, at 2.9 Å resolution. Despite a 70 Å distance, binding of Ser-SA in the catalytic domain dramatically leverages the position of Insertion I in the tRNA binding domain. Importantly, this leverage is specific to higher eukaryotes and not seen in bacterial, archaeal, and lower eukaryotic SerRSs. Deletion of Insertion I does not affect tRNA binding but instead reduce the catalytic efficiency of the synthetase. Thus, a long-range conformational and functional communication specific to higher eukaryotes is found in human SerRS, possibly to coordinate translation with vasculogenesis.

PubMed: 24095058
DOI: 10.1016/j.str.2013.08.021

Experimental method

X-RAY DIFFRACTION (2.897 Å)