2E1B

Crystal structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii

Summary for 2E1B

• Entry DOI: 10.2210/pdb2e1b/pdb
• Descriptor: 216aa long hypothetical alanyl-tRNA synthetase, ZINC ION (2 entities in total)
• Functional Keywords: zinc-binding motif, trans-editing enzyme, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, ligase, hydrolase
• Biological source: Pyrococcus horikoshii
• Cellular location: Cytoplasm (Probable): O57848
• Total number of polymer chains: 1
• Total formula weight: 25404.34

Authors

Fukunaga, R.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2006-10-20, release date: 2007-03-06, Last modification date: 2024-03-13)

Primary citation

Fukunaga, R.,Yokoyama, S.
Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii
ACTA CRYSTALLOGR.,SECT.D, 63:390-400, 2007

PubMed Abstract: The editing domain of alanyl-tRNA synthetase (AlaRS) contributes to high-fidelity aminoacylation by hydrolyzing (editing) the incorrect products Ser-tRNA(Ala) and Gly-tRNA(Ala) (cis-editing). The AlaX protein shares sequence homology to the editing domain of AlaRS. There are three types of AlaX proteins, with different numbers of amino-acid residues (AlaX-S, AlaX-M and AlaX-L). In this report, AlaX-M from Pyrococcus horikoshii is shown to deacylate Ser-tRNA(Ala) and Gly-tRNA(Ala) (trans-editing). The crystal structure of P. horikoshii AlaX-M has been determined at 2.7 A resolution. AlaX-M consists of an N-terminal domain (N-domain) and a C-terminal domain (C-domain). A zinc ion is coordinated by the conserved zinc-binding cluster in the C-domain, which is expected to be the enzymatic active site. The glycine-rich motif, consisting of successive conserved glycine residues in the N-domain, forms a loop (the 'glycine-rich loop'). The glycine-rich loop is located near the active site and may be involved in substrate recognition and/or catalysis.

PubMed: 17327676
DOI: 10.1107/S090744490605640X

Experimental method

X-RAY DIFFRACTION (2.7 Å)