1td2

Crystal Structure of the PdxY Protein from Escherichia coli

spinqualitylabelsall models 1td2, resolution 2.22Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1td2 is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.22Å Ligands: PXL, SO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function PDXY_ECOLI Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxamine, but has negligible activity toward pyridoxal and pyridoxine as substrates.[HAMAP-Rule:MF_01639] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. Crystal structure of the PdxY Protein from Escherichia coli.,Safo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V J Bacteriol. 2004 Dec;186(23):8074-82. PMID:15547280 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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