PDBsum entry 2efx

Hydrolase

PDB id: 2efx

Contents

Protein chains

362 a.a. *

296 a.a. *

Ligands

NFA ×6

Metals

_BA ×22

Waters ×1188

* Residue conservation analysis

PDB id:

2efx

Name:

Hydrolase

Title:

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

Structure:

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

Source:

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

Resolution:

2.20Å R-factor: 0.190 R-free: 0.256

Authors:

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

Key ref:

S.Okazaki et al. (2008). Structures of D-amino-acid amidase complexed with L-phenylalanine and with L-phenylalanine amide: insight into the D-stereospecificity of D-amino-acid amidase from Ochrobactrum anthropi SV3. Acta Crystallogr D Biol Crystallogr, 64, 331-334. PubMed id: 18323628 DOI: 10.1107/S0907444907067479

Date:

26-Feb-07 Release date: 06-Mar-07

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: 296 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DOI no: 10.1107/S0907444907067479

Acta Crystallogr D Biol Crystallogr 64:331-334 (2008)

PubMed id: 18323628

Structures of D-amino-acid amidase complexed with L-phenylalanine and with L-phenylalanine amide: insight into the D-stereospecificity of D-amino-acid amidase from Ochrobactrum anthropi SV3.

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

ABSTRACT

The crystal structures of D-amino-acid amidase (DAA) from Ochrobactrum anthropi SV3 in complex with L-phenylalanine and with L-phenylalanine amide were determined at 2.3 and 2.2 A resolution, respectively. Comparison of the L-phenylalanine amide complex with the D-phenylalanine complex reveals that the D-stereospecificity of DAA might be achieved as a consequence of three structural factors: (i) the hydrophobic cavity in the region in which the hydrophobic side chain of the substrate is held, (ii) the spatial arrangement of Gln310 O and Glu114 O epsilon2 that fixes the amino N atom of the substrate and (iii) the existence of two cavities that keep the carboxyl/amide group of the substrate near or apart from Ser60 O gamma.

Selected figure(s)

Figure 2.
Figure 2 (a) Active-site residues of molecule A (ordered type) of the L-Phe-NH[2] complex. C atoms are shown in grey, O atoms in red and N atoms in blue. A [A]-weighted F[o] - F[c] L-Phe-NH[2] OMIT map contoured at 3.0 is superposed in grey. Broken red lines represent hydrogen bonds. (b) Active-site residues of moleucle E (disordered type) of the L-Phe-NH[2] complex. C atoms are shown in light green. [A]-Weighted F[o] - F[c] L-Phe-NH[2] OMIT maps contoured at 3.0 and 2.0 are superposed in grey and cyan, respectively. (c) Stereoview of the superposition of the active-site residues of molecule E in the L-Phe-NH[2] complex and those in the D-Phe complex. The hypothetical mirror plane is shown as a black line. For the L-Phe-NH[2] complex, C atoms are shown in light green and hydrogen bonds are shown as red broken lines. For the D-Phe complex, C atoms are shown in pink and hydrogen bonds are shown as magenta broken lines. (d) Schematic representation of the binding mode of L-Phe-NH[2] and D-Phe in molecule E of DAA. L-Phe-NH[2] and D-Phe are shown in red. The hydrophobic cavity for holding the side chain and the space for anchoring the amino N atom are labelled (1) and (2), respectively. The cavities in which the amide group of L-Phe-NH[2] and the carboxyl group of D-Phe are located are labelled (3L) and (3D), respectively.

The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 331-334) copyright 2008.

Figure was selected by an automated process.