1FO6

CRYSTAL STRUCTURE ANALYSIS OF N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE

Summary for 1FO6

• Entry DOI: 10.2210/pdb1fo6/pdb
• Descriptor: N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE, XENON (3 entities in total)
• Functional Keywords: four layer a/b fold, hydrolase
• Biological source: Agrobacterium tumefaciens
• Total number of polymer chains: 4
• Total formula weight: 137098.83

Authors

Wang, W.-C.,Hsu, W.-H.,Chien, F.-T.,Chen, C.-Y. (deposition date: 2000-08-25, release date: 2001-08-29, Last modification date: 2024-03-13)

Primary citation

Wang, W.C.,Hsu, W.H.,Chien, F.T.,Chen, C.Y.
Crystal structure and site-directed mutagenesis studies of N-carbamoyl-D-amino-acid amidohydrolase from Agrobacterium radiobacter reveals a homotetramer and insight into a catalytic cleft.
J.Mol.Biol., 306:251-261, 2001

PubMed Abstract: The N-carbamoyl-D-amino-acid amidohydrolase (D-NCAase) is used on an industrial scale for the production of D-amino acids. The crystal structure of D-NCAase was solved by multiple isomorphous replacement with anomalous scattering using xenon and gold derivatives, and refined to 1.95 A resolution, to an R-factor of 18.6 %. The crystal structure shows a four-layer alpha/beta fold with two six-stranded beta sheets packed on either side by two alpha helices. One exterior layer faces the solvent, whereas the other one is buried and involved in the tight intersubunit contacts. A long C-terminal fragment extends from a monomer to a site near a dyad axis, and associates with another monomer to form a small and hydrophobic cavity, where a xenon atom can bind. Site-directed mutagenesis of His129, His144 and His215 revealed strict geometric requirements of these conserved residues to maintain a stable conformation of a putative catalytic cleft. A region located within this cleft involving Cys172, Glu47, and Lys127 is proposed for D-NCAase catalysis and is similar to the Cys-Asp-Lys site of N-carbamoylsarcosine amidohydrolase. The homologous active-site framework of these enzymes with distinct structures suggests convergent evolution of a common catalytic mechanism.

PubMed: 11237598
DOI: 10.1006/jmbi.2000.4380

Experimental method

X-RAY DIFFRACTION (1.95 Å)