6KDI

Antibody 64M-5 Fab including isoAsp in complex with dT(6-4)T

6KDI の概要

• エントリーDOI: 10.2210/pdb6kdi/pdb
• 分子名称: Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), DNA (5'-D(*(64T)P*(5PY))-3'), ... (4 entities in total)
• 機能のキーワード: dna (6-4) photoproduct, immunoglobulin, fab, immune system, isoaspartate
• 由来する生物種: Mus musculus; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 48491.78

構造登録者

Yokoyama, H.,Mizutani, R.,Noguchi, S.,Hayashida, N. (登録日: 2019-07-02, 公開日: 2019-12-18, 最終更新日: 2024-10-30)

主引用文献

Yokoyama, H.,Mizutani, R.,Noguchi, S.,Hayashida, N.
Structural and biochemical basis of the formation of isoaspartate in the complementarity-determining region of antibody 64M-5 Fab.
Sci Rep, 9:18494-18494, 2019

PubMed Abstract: The formation of the isoaspartate (isoAsp) is one of spontaneous degradation processes of proteins, affecting their stability and activity. Here, we report for the first time the crystal structures of an antibody Fab that contains isoAsp in the complementarity-determining region (CDR), along with biochemical studies to detect isoAsp. By comparing the elution profiles of cation-exchange chromatography, it was clarified that the antibody 64M-5 Fab is converted from the normal form to isoAsp form spontaneously and time-dependently under physiological conditions. The isoAsp residue was identified with tryptic peptide mapping, N-terminal sequencing, and the protein isoaspartyl methyltransferase assay. Based on the fluorescence quenching method, the isoAsp form of 64M-5 Fab shows a one order of magnitude lower binding constant for its dinucleotide ligand dT(6-4)T than the normal form. According to the structure of the isoAsp form, the conformation of CDR L1 is changed from the normal form to isoAsp form; the loss of hydrogen bonds involving the Asn28L side-chain, and structural conversion of the β-turn from type I to type II'. The formation of isoAsp leads to a large displacement of the side chain of His27dL, and decreased electrostatic interactions with the phosphate group of dT(6-4)T. Such structural changes should be responsible for the lower affinity of the isoAsp form for dT(6-4)T than the normal form. These findings may provide insight into neurodegenerative diseases (NDDs) and related diseases caused by misfolded proteins.

PubMed: 31811216
DOI: 10.1038/s41598-019-54918-0

実験手法

X-RAY DIFFRACTION (2.7 Å)