1B65

Structure of l-aminopeptidase d-ala-esterase/amidase from ochrobactrum anthropi, a prototype for the serine aminopeptidases, reveals a new variant among the ntn hydrolase fold

• PDB DOI: https://doi.org/10.2210/pdb1B65/pdb

• Classification: HYDROLASE
• Organism(s): Brucella anthropi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-01-20 Released: 1999-07-23 
• Deposition Author(s): Bompard-Gilles, C., Villeret, V., Davies, G.J., Fanuel, L., Joris, B., Frere, J.M., Van Beeumen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.206 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Literature

A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi.

Bompard-Gilles, C., Villeret, V., Davies, G.J., Fanuel, L., Joris, B., Frere, J.M., Van Beeumen, J.

(2000) Structure 8: 153-162

• PubMed: 10673442 
• DOI: https://doi.org/10.1016/s0969-2126(00)00091-5
• Primary Citation of Related Structures:  
  1B65


• PubMed Abstract: 
  

  The L-aminopeptidase D-Ala-esterase/amidase from Ochrobactrum anthropi (DmpA) releases the N-terminal L and/or D-Ala residues from peptide substrates. This is the only known enzyme to liberate N-terminal amino acids with both D and L stereospecificity. The DmpA active form is an alphabeta heterodimer, which results from a putative autocatalytic cleavage of an inactive precursor polypeptide.

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Organizational Affiliation: 

Laboratorium voor Eiwitbiochemie en Eiwitengineering, Rijksuniversiteit-Gent, Gent, B-9000, Belgium.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 242.75 kDa 
• Atom Count: 17,786 
• Modelled Residue Count: 2,178 
• Deposited Residue Count: 2,250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (AMINOPEPTIDASE)	A, B, C, D, E, F	375	Brucella anthropi	Mutation(s): 0
UniProt
Find proteins for Q59632 (Brucella anthropi) Explore Q59632  Go to UniProtKB:  Q59632

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.206 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.97	α = 90
b = 96.22	β = 90
c = 154.41	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	model building
REFMAC	refinement
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-23 
Deposition Author(s): Bompard-Gilles, C., Villeret, V., Davies, G.J., Fanuel, L., Joris, B., Frere, J.M., Van Beeumen, J.

Revision History  

• Version 1.0: 1999-07-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references