2ZVF

Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain

Summary for 2ZVF

• Entry DOI: 10.2210/pdb2zvf/pdb
• Related: 2ZTG
• Descriptor: Alanyl-tRNA synthetase, SULFATE ION (3 entities in total)
• Functional Keywords: alanyl-trna synthetase, c-terminal, oligomerization domain, aminoacyl-trna synthetase, atp-binding, cytoplasm, ligase, nucleotide-binding, protein biosynthesis, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi
• Biological source: Archaeoglobus fulgidus
• Cellular location: Cytoplasm: O28029
• Total number of polymer chains: 8
• Total formula weight: 157596.00

Authors

Naganuma, M.,Sekine, S.,Fukunaga, R.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2008-11-06, release date: 2009-06-30, Last modification date: 2024-10-30)

Primary citation

Naganuma, M.,Sekine, S.,Fukunaga, R.,Yokoyama, S.
Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.
Proc.Natl.Acad.Sci.USA, 106:8489-8494, 2009

PubMed Abstract: Alanyl-tRNA synthetase (AlaRS) specifically recognizes the major identity determinant, the G3:U70 base pair, in the acceptor stem of tRNA(Ala) by both the tRNA-recognition and editing domains. In this study, we solved the crystal structures of 2 halves of Archaeoglobus fulgidus AlaRS: AlaRS-DeltaC, comprising the aminoacylation, tRNA-recognition, and editing domains, and AlaRS-C, comprising the dimerization domain. The aminoacylation/tRNA-recognition domains contain an insertion incompatible with the class-specific tRNA-binding mode. The editing domain is fixed tightly via hydrophobic interactions to the aminoacylation/tRNA-recognition domains, on the side opposite from that in threonyl-tRNA synthetase. A groove formed between the aminoacylation/tRNA-recognition domains and the editing domain appears to be an alternative tRNA-binding site, which might be used for the aminoacylation and/or editing reactions. Actually, the amino acid residues required for the G3:U70 recognition are mapped in this groove. The dimerization domain consists of helical and globular subdomains. The helical subdomain mediates dimerization by forming a helix-loop-helix zipper. The globular subdomain, which is important for the aminoacylation and editing activities, has a positively-charged face suitable for tRNA binding.

PubMed: 19423669
DOI: 10.1073/pnas.0901572106

Experimental method

X-RAY DIFFRACTION (3.2 Å)