title: The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, alpha-amino-epsilon-caprolactam racemase from Achromobacter obae.
abstract: Alpha-amino-epsilon-caprolactam (ACL) racemase (ACLR) from Achromobacter obae catalyzes the interconversion of l- and d-ACL. ACLR belongs to the fold-type I group of pyridoxal 5'-phosphate (PLP) dependent enzymes. In this study, the first crystal structures of a fold-type I racemase are solved for the native form and epsilon-caprolactam-complexed form of ACLR at 2.21 and 2.40 A resolution, respectively. Based on the location of epsilon-caprolactam in the complex structure, the substrate-binding site is assigned between Trp49 and Tyr137. The carboxyl group of Asp210 is a reasonable candidate that recognizes the nitrogen atom of a lactam or amide in the substrate. Based on a structural comparison with fold-type III alanine racemase, Tyr137 is potentially the acid/base catalytic residue that is essential for the two-base racemization mechanism. The overall structure of ACLR is similar to that of fold-type I enzymes. A structural comparison with these enzymes explains the different reaction specificities.
authors.affiliation: Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan.
authors.forename: Seiji
authors.initials: S
authors.lastname: Okazaki
authors.forename: Atsuo
authors.initials: A
authors.lastname: Suzuki
authors.forename: Tsunehiro
authors.initials: T
authors.lastname: Mizushima
authors.forename: Takeshi
authors.initials: T
authors.lastname: Kawano
authors.forename: Hidenobu
authors.initials: H
authors.lastname: Komeda
authors.forename: Yasuhisa
authors.initials: Y
authors.lastname: Asano
authors.forename: Takashi
authors.initials: T
authors.lastname: Yamane
mesh_terms: D042402:Achromobacter / Q000201:enzymology*; D000591:Amino Acid Isomerases / Q000737:chemistry*; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D017510:Protein Folding; D011732:Pyridoxal Phosphate / Q000737:chemistry*; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D011732:Pyridoxal Phosphate; D000591:Amino Acid Isomerases; C036861:aminocaprolactam racemase