PDBsum entry 2dns

Hydrolase

PDB id: 2dns

Contents

Protein chains

362 a.a. *

300 a.a. *

Ligands

DPN ×5

Metals

_BA ×20

Waters ×745

* Residue conservation analysis

PDB id:

2dns

Name:

Hydrolase

Title:

The crystal structure of d-amino acid amidase from ochrobactrum anthropi sv3 complexed with d-phenylalanine

Structure:

D-amino acid amidase. Chain: a, b, c, d, e, f. Engineered: yes

Source:

Ochrobactrum anthropi. Organism_taxid: 529. Strain: sv3. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.199 R-free: 0.269

Authors:

S.Okazaki,A.Suzuki,H.Komeda,Y.Asano,T.Yamane

Key ref:

S.Okazaki et al. (2007). 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. PubMed id: 17331533 DOI: 10.1016/j.jmb.2006.10.070

Date:

26-Apr-06 Release date: 09-May-06

Supersedes:

2dd0

Protein chains

Q9LCC8  (Q9LCC8_BRUAN) -  D-Amino acid amidase from Brucella anthropi

Seq: 363 a.a.

Struc: 362 a.a.

Protein chain

Q9LCC8  (Q9LCC8_BRUAN) -  D-Amino acid amidase from Brucella anthropi

Seq: 363 a.a.

Struc: 300 a.a.

DOI no: 10.1016/j.jmb.2006.10.070

J Mol Biol 368:79-91 (2007)

PubMed id: 17331533

Crystal structure and functional characterization of a D-stereospecific amino acid amidase from Ochrobactrum anthropi SV3, a new member of the penicillin-recognizing proteins.

S.Okazaki, A.Suzuki, H.Komeda, S.Yamaguchi, Y.Asano, T.Yamane.

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.

Selected figure(s)

Figure 3.
Figure 3. Electrostatic potential surface and active-site pocket in the native structure. Red and blue indicate negative and positive electrostatic potentials, respectively. Hydrophobic (green) and hydrophilic (cyan) capacities are represented as an assembly of ball and stick dummy atoms, respectively. (a) Electrostatic potential surface of subunit A. The main chain of the Ω-loop (residues 207–223) and the side-chain of Trp215, colored purple, are superimposed. (b) Electrostatic potential surface of subunit E. Glu114 and the newly formed hydrophobic capacity are highlighted.

Figure 8.
Figure 8. The proposed reaction mechanism for deacylation by DAA at pH 6.8. d-Phenylalanine is shown in red. Hydrogen bonds are represented as broken lines. The orientation of the His307 side-chain found in subunit F is shown.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 368, 79-91) copyright 2007.

Figures were selected by an automated process.