1TD2

Crystal Structure of the PdxY Protein from Escherichia coli

1TD2 の概要

• エントリーDOI: 10.2210/pdb1td2/pdb
• 分子名称: Pyridoxamine kinase, 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE, SULFATE ION, ... (4 entities in total)
• 機能のキーワード: pyridoxal kinase, ribokinase family, kinase, phosphorylation, pdxy, transferase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 63146.72

構造登録者

Safo, M.K.,Musayev, F.N.,Hunt, S.,di Salvo, M.,Scarsdale, N.,Schirch, V. (登録日: 2004-05-21, 公開日: 2004-07-13, 最終更新日: 2024-11-20)

主引用文献

Safo, M.K.,Musayev, F.N.,Hunt, S.,di Salvo, M.L.,Scarsdale, N.,Schirch, V.
Crystal structure of the PdxY Protein from Escherichia coli
J.Bacteriol., 186:8074-8082, 2004

PubMed Abstract: The crystal structure of Escherichia coli PdxY, the protein product of the pdxY gene, has been determined to a 2.2-A resolution. PdxY is a member of the ribokinase superfamily of enzymes and has sequence homology with pyridoxal kinases that phosphorylate pyridoxal at the C-5' hydroxyl. The protein is a homodimer with an active site on each monomer composed of residues that come exclusively from each respective subunit. The active site is filled with a density that fits that of pyridoxal. In monomer A, the ligand appears to be covalently attached to Cys122 as a thiohemiacetal, while in monomer B it is not covalently attached but appears to be partially present as pyridoxal 5'-phosphate. The presence of pyridoxal phosphate and pyridoxal as ligands was confirmed by the activation of aposerine hydroxymethyltransferase after release of the ligand by the denaturation of PdxY. The ligand, which appears to be covalently attached to Cys122, does not dissociate after denaturation of the protein. A detailed comparison (of functional properties, sequence homology, active site and ATP-binding-site residues, and active site flap types) of PdxY with other pyridoxal kinases as well as the ribokinase superfamily in general suggested that PdxY is a member of a new subclass of the ribokinase superfamily. The structure of PdxY also permitted an interpretation of work that was previously published about this enzyme.

PubMed: 15547280
DOI: 10.1128/JB.186.23.8074-8082.2004

実験手法

X-RAY DIFFRACTION (2.22 Å)