Structural motifs for pyridoxal-5'-phosphate binding in decarboxylases: an analysis based on the crystal structure of the Lactobacillus 30a ornithine decarboxylase.
Two of the five domains in the structure of the ornithine decarboxylase (OrnDC) from Lactobacillus 30a share similar structural folds around the pyridoxal-5'-phosphate (PLP)-binding pocket with the aspartate aminotransferases (AspATs). Sequence comparisons focusing on conserved residues of the aligned structures reveal that this structural motif is also present in a number of other PLP-dependent enzymes including the histidine, dopa, tryptophan, glutamate, and glycine decarboxylases as well as tryptophanase and serine-hydroxymethyl transferase. However, this motif is not present in eukaryotic OrnDCs, the diaminopimelate decarboxylases, nor the Escherichia coli or oat arginine decarboxylases. The identification and comparison of residues involved in defining the different classes are discussed.
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Department of Chemistry and Biochemistry, University of Texas at Austin 78712, USA.
Ghosh
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Hackert
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D000595:Amino Acid Sequence; D001219:Aspartate Aminotransferases / Q000737:chemistry; D005075:Biological Evolution; D002262:Carboxy-Lyases / Q000737:chemistry / Q000378:metabolism; D003196:Computer Graphics; D017124:Conserved Sequence; D007778:Lactobacillus / Q000201:enzymology*; D008969:Molecular Sequence Data; D009955:Ornithine Decarboxylase / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011732:Pyridoxal Phosphate / Q000378:metabolism*; D016415:Sequence Alignment
D011732:Pyridoxal Phosphate; D001219:Aspartate Aminotransferases; D002262:Carboxy-Lyases; D009955:Ornithine Decarboxylase