3WCO

Crystal structure of the depentamerized mutant of N-terminal truncated selenocysteine synthase SelA

Summary for 3WCO

• Entry DOI: 10.2210/pdb3wco/pdb
• Related: 3W1H 3W1I 3W1J 3W1K 3WCN
• Descriptor: L-seryl-tRNA(Sec) selenium transferase, THIOSULFATE (3 entities in total)
• Functional Keywords: fold-type-i pyridoxal 5'-phosphate (plp) dependent enzyme, homodimer, l-seryl-trna(sec) selenium transferase, selenocysteine synthesis, selenium metabolism, transferase
• Biological source: Aquifex aeolicus
• Cellular location: Cytoplasm (By similarity): O67140
• Total number of polymer chains: 2
• Total formula weight: 89507.54

Authors

Itoh, Y.,Sekine, S.,Yokoyama, S. (deposition date: 2013-05-29, release date: 2014-01-22, Last modification date: 2023-12-06)

Primary citation

Itoh, Y.,Brocker, M.J.,Sekine, S.,Soll, D.,Yokoyama, S.
Dimer-Dimer Interaction of the Bacterial Selenocysteine Synthase SelA Promotes Functional Active-Site Formation and Catalytic Specificity
J.Mol.Biol., 426:1723-1735, 2014

PubMed Abstract: The 21st amino acid, selenocysteine (Sec), is incorporated translationally into proteins and is synthesized on its specific tRNA (tRNA(Sec)). In Bacteria, the selenocysteine synthase SelA converts Ser-tRNA(Sec), formed by seryl-tRNA synthetase, to Sec-tRNA(Sec). SelA, a member of the fold-type-I pyridoxal 5'-phosphate-dependent enzyme superfamily, has an exceptional homodecameric quaternary structure with a molecular mass of about 500kDa. Our previously determined crystal structures of Aquifex aeolicus SelA complexed with tRNA(Sec) revealed that the ring-shaped decamer is composed of pentamerized SelA dimers, with two SelA dimers arranged to collaboratively interact with one Ser-tRNA(Sec). The SelA catalytic site is close to the dimer-dimer interface, but the significance of the dimer pentamerization in the catalytic site formation remained elusive. In the present study, we examined the quaternary interactions and demonstrated their importance for SelA activity by systematic mutagenesis. Furthermore, we determined the crystal structures of "depentamerized" SelA variants with mutations at the dimer-dimer interface that prevent pentamerization. These dimeric SelA variants formed a distorted and inactivated catalytic site and confirmed that the pentamer interactions are essential for productive catalytic site formation. Intriguingly, the conformation of the non-functional active site of dimeric SelA shares structural features with other fold-type-I pyridoxal 5'-phosphate-dependent enzymes with native dimer or tetramer (dimer-of-dimers) quaternary structures.

PubMed: 24456689
DOI: 10.1016/j.jmb.2014.01.003

Experimental method

X-RAY DIFFRACTION (2.4 Å)