1DDT

THE REFINED STRUCTURE OF DIMERIC DIPHTHERIA TOXIN AT 2.0 ANGSTROMS RESOLUTION

1DDT の概要

• エントリーDOI: 10.2210/pdb1ddt/pdb
• 分子名称: DIPHTHERIA TOXIN, ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE (3 entities in total)
• 機能のキーワード: toxin
• 由来する生物種: Corynephage beta
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 59064.75

構造登録者

Bennett, M.J.,Eisenberg, D. (登録日: 1994-03-01, 公開日: 1994-07-31, 最終更新日: 2024-11-20)

主引用文献

Bennett, M.J.,Choe, S.,Eisenberg, D.
Refined structure of dimeric diphtheria toxin at 2.0 A resolution.
Protein Sci., 3:1444-1463, 1994

PubMed Abstract: The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution, based on 37,727 unique reflections (F > 1 sigma (F)), yields a final R factor of 19.5% with a model obeying standard geometry. The refined model consists of 523 amino acid residues, 1 molecule of the bound dinucleotide inhibitor adenylyl 3'-5' uridine 3' monophosphate (ApUp), and 405 well-ordered water molecules. The 2.0-A refined model reveals that the binding motif for ApUp includes residues in the catalytic and receptor-binding domains and is different from the Rossmann dinucleotide-binding fold. ApUp is bound in part by a long loop (residues 34-52) that crosses the active site. Several residues in the active site were previously identified as NAD-binding residues. Glu 148, previously identified as playing a catalytic role in ADP-ribosylation of elongation factor 2 by DT, is about 5 A from uracil in ApUp. The trigger for insertion of the transmembrane domain of DT into the endosomal membrane at low pH may involve 3 intradomain and 4 interdomain salt bridges that will be weakened at low pH by protonation of their acidic residues. The refined model also reveals that each molecule in dimeric DT has an "open" structure unlike most globular proteins, which we call an open monomer. Two open monomers interact by "domain swapping" to form a compact, globular dimeric DT structure. The possibility that the open monomer resembles a membrane insertion intermediate is discussed.

PubMed: 7833807

実験手法

X-RAY DIFFRACTION (2 Å)