The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes. 1998

M S Hasson, and A Muscate, and M J McLeish, and L S Polovnikova, and J A Gerlt, and G L Kenyon, and G A Petsko, and D Ringe
Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.

The crystal structure of the thiamin diphosphate (ThDP)-dependent enzyme benzoylformate decarboxylase (BFD), the third enzyme in the mandelate pathway of Pseudomonas putida, has been solved by multiple isomorphous replacement at 1.6 A resolution and refined to an R-factor of 15.0% (free R = 18.6%). The structure of BFD has been compared to that of other ThDP-dependent enzymes, including pyruvate decarboxylase. The overall architecture of BFD resembles that of the other family members, and cofactor- and metal-binding residues are well conserved. Surprisingly, there is no conservation of active-site residues not directly bound to the cofactor. The position of functional groups in the active site may be conserved, however. Three classes of metal ions have been identified in the BFD crystal structure: Ca2+ bound to the cofactor in each subunit, Mg2+ on a 2-fold axis of the tetramer, and Ca2+ at a crystal contact. The structure includes a non-proline cis-peptide bond and an unusually long and regular polyproline type II helix that mediates the main contact between tetramers in the crystal. The high-quality electron-density map allowed the correction of errors totaling more than 10% of the amino acid sequence, which had been predicted from the reported sequence of the mdlC gene. Analysis of the BFD structure suggests that requirements for activation of the cofactor, the nature of the reaction intermediates, and architectural considerations relating to the protein fold have been dominant forces in the evolution of ThDP-dependent enzymes.

UI MeSH Term Description Entries
D008274 Magnesium A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D010455 Peptides Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are considered to be larger versions of peptides that can form into complex structures such as ENZYMES and RECEPTORS. Peptide,Polypeptide,Polypeptides
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D002118 Calcium A basic element found in nearly all tissues. It is a member of the alkaline earth family of metals with the atomic symbol Ca, atomic number 20, and atomic weight 40. Calcium is the most abundant mineral in the body and combines with phosphorus to form calcium phosphate in the bones and teeth. It is essential for the normal functioning of nerves and muscles and plays a role in blood coagulation (as factor IV) and in many enzymatic processes. Coagulation Factor IV,Factor IV,Blood Coagulation Factor IV,Calcium-40,Calcium 40,Factor IV, Coagulation
D002262 Carboxy-Lyases Enzymes that catalyze the addition of a carboxyl group to a compound (carboxylases) or the removal of a carboxyl group from a compound (decarboxylases). EC 4.1.1. Carboxy-Lyase,Decarboxylase,Decarboxylases,Carboxy Lyase,Carboxy Lyases
D002384 Catalysis The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction. Catalyses
D002413 Cations, Divalent Positively charged atoms, radicals or groups of atoms with a valence of plus 2, which travel to the cathode or negative pole during electrolysis. Divalent Cations
D003460 Crystallization The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Crystalline Polymorphs,Polymorphism, Crystallization,Crystal Growth,Polymorphic Crystals,Crystal, Polymorphic,Crystalline Polymorph,Crystallization Polymorphism,Crystallization Polymorphisms,Crystals, Polymorphic,Growth, Crystal,Polymorph, Crystalline,Polymorphic Crystal,Polymorphisms, Crystallization,Polymorphs, Crystalline

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