3DXV

The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae

Summary for 3DXV

• Entry DOI: 10.2210/pdb3dxv/pdb
• Related: 3DXW
• Descriptor: Alpha-amino-epsilon-caprolactam racemase, PYRIDOXAL-5'-PHOSPHATE (3 entities in total)
• Functional Keywords: fold-type1, pyridoxal-5'-phosphate dependent racemase, pyridoxal phosphate, isomerase
• Biological source: Achromobacter obae
• Total number of polymer chains: 2
• Total formula weight: 92557.23

Authors

Okazaki, S.,Suzuki, A.,Komeda, H.,Asano, Y.,Yamane, T. (deposition date: 2008-07-25, release date: 2009-02-17, Last modification date: 2023-11-01)

Primary citation

Okazaki, S.,Suzuki, A.,Mizushima, T.,Kawano, T.,Komeda, H.,Asano, Y.,Yamane, T.
The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, alpha-amino-epsilon-caprolactam racemase from Achromobacter obae
Biochemistry, 48:941-950, 2009

PubMed 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.

PubMed: 19146406
DOI: 10.1021/bi801574p

Experimental method

X-RAY DIFFRACTION (2.21 Å)