3W20

Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD

3W20 の概要

• エントリーDOI: 10.2210/pdb3w20/pdb
• 関連するPDBエントリー: 3W21
• 分子名称: Putative uncharacterized protein, ZINC ION (3 entities in total)
• 機能のキーワード: dsbh fold, dioxygenase, zn, alpha-kg binding, oxidoreductase
• 由来する生物種: Burkholderia ambifaria
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 62475.89

構造登録者

Qin, H.M.,Miyakawa, T.,Jia, M.Z.,Nakamura, A.,Ohtsuka, J.,Xue, Y.L.,Kawashima, T.,Kasahara, T.,Hibi, M.,Ogawa, J.,Tanokura, M. (登録日: 2012-11-26, 公開日: 2013-07-17, 最終更新日: 2024-10-30)

主引用文献

Qin, H.M.,Miyakawa, T.,Jia, M.Z.,Nakamura, A.,Ohtsuka, J.,Xue, Y.L.,Kawashima, T.,Kasahara, T.,Hibi, M.,Ogawa, J.,Tanokura, M.
Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD
Plos One, 8:e63996-e63996, 2013

PubMed Abstract: A novel dioxygenase from Burkholderia ambifaria AMMD (SadA) stereoselectively catalyzes the C3-hydroxylation of N-substituted branched-chain or aromatic L-amino acids, especially N-succinyl-L-leucine, coupled with the conversion of α-ketoglutarate to succinate and CO2. To elucidate the structural basis of the substrate specificity and stereoselective hydroxylation, we determined the crystal structures of the SadA.Zn(II) and SadA.Zn(II).α-KG complexes at 1.77 Å and 1.98 Å resolutions, respectively. SadA adopted a double-stranded β-helix fold at the core of the structure. In addition, an HXD/EXnH motif in the active site coordinated a Zn(II) as a substitute for Fe(II). The α-KG molecule also coordinated Zn(II) in a bidentate manner via its 1-carboxylate and 2-oxo groups. Based on the SadA.Zn(II).α-KG structure and mutation analyses, we constructed substrate-binding models with N-succinyl-L-leucine and N-succinyl-L-phenylalanine, which provided new insight into the substrate specificity. The results will be useful for the rational design of SadA variants aimed at the recognition of various N-succinyl L-amino acids.

PubMed: 23724013
DOI: 10.1371/journal.pone.0063996

実験手法

X-RAY DIFFRACTION (1.77 Å)