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PDBsum entry 1td2
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the pdxy protein from escherichia coli.
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Authors
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M.K.Safo,
F.N.Musayev,
S.Hunt,
M.L.Di salvo,
N.Scarsdale,
V.Schirch.
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Ref.
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J Bacteriol, 2004,
186,
8074-8082.
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PubMed id
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Abstract
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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.
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