Gene identification and structural characterization of the PLP degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from Mesorhizobium loti MAFF303099

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 B 6 ). 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 K M and k cat were found to be 366 μ M and 0.6 s -1 respectively. The structure of this enzyme was determined at 1.9 Å 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. residues in close proximity to each other: His27, His92, His94, His163, and His177 from one subunit and His113* from the neighboring subunit.

[1]  C. Kinsland,et al.  PLP catabolism: identification of the 4-pyridoxic acid dehydrogenase gene in Mesorhizobium loti MAFF303099. , 2007, Bioorganic chemistry.

[2]  Eric Blanc,et al.  Automated structure solution with autoSHARP. , 2007, Methods in molecular biology.

[3]  K. Ohnishi,et al.  Molecular cloning, identification and characterization of 2-methyl-3-hydroxypyridine-5-carboxylic-acid-dioxygenase-coding gene from the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. , 2006, Journal of bioscience and bioengineering.

[4]  K. Ohnishi,et al.  Identification of a new tetrameric pyridoxal 4-dehydrogenase as the second enzyme in the degradation pathway for pyridoxine in a nitrogen-fixing symbiotic bacterium, Mesorhizobium loti. , 2006, Archives of biochemistry and biophysics.

[5]  K. Ohnishi,et al.  4-Pyridoxolactonase from a symbiotic nitrogen-fixing bacterium Mesorhizobium loti: cloning, expression, and characterization. , 2005, Biochimica et biophysica acta.

[6]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[7]  T. Begley,et al.  Enzymatic reactions involving novel mechanisms of carbanion stabilization. , 2004, Current opinion in chemical biology.

[8]  K. Ohnishi,et al.  The nitrogen-fixing symbiotic bacterium Mesorhizobium loti has and expresses the gene encoding pyridoxine 4-oxidase involved in the degradation of vitamin B6. , 2004, FEMS microbiology letters.

[9]  T. Omori,et al.  Phthalate catabolic gene cluster is linked to the angular dioxygenase gene in Terrabacter sp. strain DBF63 , 2003, Applied Microbiology and Biotechnology.

[10]  G. Schulz,et al.  The structure of L-rhamnulose-1-phosphate aldolase (class II) solved by low-resolution SIR phasing and 20-fold NCS averaging. , 2002, Acta crystallographica. Section D, Biological crystallography.

[11]  Richard Wolfenden,et al.  Catalytic proficiency: the unusual case of OMP decarboxylase. , 2002, Annual review of biochemistry.

[12]  Y. Luo,et al.  The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization. , 2001, Biochemistry.

[13]  Y. Luo,et al.  Catalysis and binding in L-ribulose-5-phosphate 4-epimerase: a comparison with L-fuculose-1-phosphate aldolase. , 2001, Biochemistry.

[14]  R. Eaton.  Plasmid-Encoded Phthalate Catabolic Pathway in Arthrobacter keyseri 12B , 2001, Journal of bacteriology.

[15]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[16]  Patrice Gouet,et al.  ESPript: analysis of multiple sequence alignments in PostScript , 1999, Bioinform..

[17]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[18]  Chris Sander,et al.  Touring protein fold space with Dali/FSSP , 1998, Nucleic Acids Res..

[19]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[20]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[21]  G. Schulz,et al.  Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure. , 1996, Journal of molecular biology.

[22]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[23]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[24]  W. C. Still,et al.  A rapid approximation to the solvent accessible surface areas of atoms , 1988 .

[25]  G. Kishore,et al.  The bacterial oxidation of vitamin B6. 4-Pyridoxic acid dehydrogenase: a membrane-bound enzyme from Pseudomonas MA-1. , 1983, The Journal of biological chemistry.

[26]  H. Krebs.  Comprehensive biochemistry , 1975, Nature.

[27]  B. Matthews.  Solvent content of protein crystals. , 1968, Journal of molecular biology.

[28]  F. Lynen,et al.  [BACTERIAL OXIDATION OF VITAMIN B6. IV. ENZYMATIC DECARBOXYLATION OF 2-METHYL-3-HYDROXYPYRIDINE-4,5-DICARBOXYLIC ACID]. , 1964, Biochemische Zeitschrift.

[29]  B. Volcani,et al.  Bacterial oxidation of vitamin B6. I. Isopyridoxal and 5-pyridoxic acid. , 1958, The Journal of biological chemistry.