2DNS

The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with D-Phenylalanine

Replaces:  2DD0

Summary for 2DNS

• Entry DOI: 10.2210/pdb2dns/pdb
• Related: 2D83
• Descriptor: D-amino acid amidase, BARIUM ION, D-PHENYLALANINE, ... (4 entities in total)
• Functional Keywords: d-stereospecific, amidase, d-phenylalanine, penicillin recognize protein, hydrolase
• Biological source: Ochrobactrum anthropi
• Total number of polymer chains: 6
• Total formula weight: 244335.63

Authors

Okazaki, S.,Suzuki, A.,Komeda, H.,Asano, Y.,Yamane, T. (deposition date: 2006-04-26, release date: 2006-05-09, Last modification date: 2024-11-20)

Primary citation

Okazaki, S.,Suzuki, A.,Komeda, H.,Yamaguchi, S.,Asano, Y.,Yamane, T.
Crystal Structure and Functional Characterization of a D-Stereospecific Amino Acid Amidase from Ochrobactrum anthropi SV3, a New Member of the Penicillin-recognizing Proteins
J.Mol.Biol., 368:79-91, 2007

PubMed Abstract: D-amino acid amidase (DAA) from Ochrobactrum anthropi SV3, which catalyzes the stereospecific hydrolysis of D-amino acid amides to yield the D-amino acid and ammonia, has attracted increasing attention as a catalyst for the stereospecific production of D-amino acids. In order to clarify the structure-function relationships of DAA, the crystal structures of native DAA, and of the D-phenylalanine/DAA complex, were determined at 2.1 and at 2.4 A resolution, respectively. Both crystals contain six subunits (A-F) in the asymmetric unit. The fold of DAA is similar to that of the penicillin-recognizing proteins, especially D-alanyl-D-alanine-carboxypeptidase from Streptomyces R61, and class C beta-lactamase from Enterobacter cloacae strain GC1. The catalytic residues of DAA and the nucleophilic water molecule for deacylation were assigned based on these structures. DAA has a flexible Omega-loop, similar to class C beta-lactamase. DAA forms a pseudo acyl-enzyme intermediate between Ser60 O(gamma) and the carbonyl moiety of d-phenylalanine in subunits A, B, C, D, and E, but not in subunit F. The difference between subunit F and the other subunits (A, B, C, D and E) might be attributed to the order/disorder structure of the Omega-loop: the structure of this loop cannot assigned in subunit F. Deacylation of subunit F may be facilitated by the relative movement of deprotonated His307 toward Tyr149. His307 N(epsilon2) extracts the proton from Tyr149 O(eta), then Tyr149 O(eta) attacks a nucleophilic water molecule as a general base. Gln214 on the Omega-loop is essential for forming a network of water molecules that contains the nucleophilic water needed for deacylation. Although peptidase activity is found in almost all penicillin-recognizing proteins, DAA lacks peptidase activity. The lack of transpeptidase and carboxypeptidase activities may be attributed to steric hindrance of the substrate-binding pocket by a loop comprised of residues 278-290 and the Omega-loop.

PubMed: 17331533
DOI: 10.1016/j.jmb.2006.10.070

Experimental method

X-RAY DIFFRACTION (2.4 Å)