2EFU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.

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

(2008) Acta Crystallogr.,Sect.D 64: 331-334

  • DOI: 10.1107/S0907444907067479
  • Primary Citation of Related Structures:  

  • PubMed 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 comp ...

    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.


    Organizational Affiliation

    Department of Biotechnology, School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-Amino acid amidase
A, B, C, D, E, F
363Ochrobactrum anthropiMutation(s): 0 
Gene Names: daaA
Find proteins for Q9LCC8 (Ochrobactrum anthropi)
Go to UniProtKB:  Q9LCC8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE

Download SDF File 
Download CCD File 
A, B, C, D, E, F
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
BA
Query on BA

Download SDF File 
Download CCD File 
A, B, C, D, E, F
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.468α = 90.00
b = 123.274β = 104.05
c = 116.156γ = 90.00
Software Package:
Software NamePurpose
JUPITORdata collection
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2008-02-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance