2DNS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal Structure and Functional Characterization of a D-Stereospecific Amino Acid Amidase from Ochrobactrum anthropi SV3, a New Member of the Penicillin-recognizing Proteins

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

(2007) J Mol Biol 368: 79-91

  • DOI: https://doi.org/10.1016/j.jmb.2006.10.070
  • Primary Citation of Related Structures:  
    2DNS, 2DRW

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-amino acid amidase
A, B, C, D, E
A, B, C, D, E, F
363Brucella anthropiMutation(s): 0 
UniProt
Find proteins for Q9LCC8 (Brucella anthropi)
Explore Q9LCC8 
Go to UniProtKB:  Q9LCC8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LCC8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DPN
Query on DPN

Download Ideal Coordinates CCD File 
BA [auth E],
L [auth A],
O [auth B],
T [auth C],
Y [auth D]
D-PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-MRVPVSSYSA-N
BA
Query on BA

Download Ideal Coordinates CCD File 
AA [auth E]
CA [auth F]
DA [auth F]
EA [auth F]
G [auth A]
AA [auth E],
CA [auth F],
DA [auth F],
EA [auth F],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D],
Z [auth E]
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.067α = 90
b = 123.702β = 104.44
c = 116.046γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
JUPITOR210data reduction
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description