2Z7B: Crystal Structure Of Mesorhizobium Loti 3-hydroxy-2-methylpyridine-4, 5-dicarboxylate Decarboxylase

The function of the mlr6791 gene from Mesorhizobium loti MAFF303099 has been identified. This gene encodes 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase (HMPDdc), an enzyme involved in the catabolism of pyridoxal 5'-phosphate (Vitamin B6). This enzyme was overexpressed in Escherichia coli and characterized. HMPDdc is a 26 kDa protein that catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to 3-hydroxy-2-methylpyridine-5-carboxylate. The KM and kcat were found to be 366 microM and 0.6 s-1, respectively. The structure of this enzyme was determined at 1.9 A resolution using SAD phasing and belongs to the class II aldolase/adducin superfamily. While the decarboxylation of hydroxy-substituted benzene rings is a common motif in biosynthesis, the mechanism of this reaction is still poorly characterized. The structural studies described here suggest that catalysis of such decarboxylations proceeds by an aldolase-like mechanism.
PDB ID: 2Z7BDownload
MMDB ID: 60709
PDB Deposition Date: 2007/8/17
Updated in MMDB: 2012/12
Experimental Method:
x-ray diffraction
Resolution: 1.9  Å
Source Organism:
Similar Structures:
Biological Unit for 2Z7B: tetrameric; determined by author and by software (PISA)
Molecular Components in 2Z7B
Label Count Molecule
Proteins (4 molecules)
Mlr6791 Protein
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

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