3N2W

Crystal structure of the N-terminal beta-aminopeptidase BapA from Sphingosinicella xenopeptidilytica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.131 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Autoproteolytic and catalytic mechanisms for the beta-aminopeptidase BapA--a member of the Ntn hydrolase family.

Merz, T.Heck, T.Geueke, B.Mittl, P.R.Briand, C.Seebach, D.Kohler, H.P.Grutter, M.G.

(2012) Structure 20: 1850-1860

  • DOI: 10.1016/j.str.2012.07.017
  • Primary Citation of Related Structures:  
    3N33, 3N2W, 3N5I

  • PubMed Abstract: 
  • The β-aminopeptidase BapA from Sphingosinicella xenopeptidilytica belongs to the N-terminal nucleophile (Ntn) hydrolases of the DmpA-like family and has the unprecedented property of cleaving N-terminal β-amino acid residues from peptides. We determined the crystal structures of the native (αβ)₄ heterooctamer and of the 153 kDa precursor homotetramer at a resolution of 1 ...

    The β-aminopeptidase BapA from Sphingosinicella xenopeptidilytica belongs to the N-terminal nucleophile (Ntn) hydrolases of the DmpA-like family and has the unprecedented property of cleaving N-terminal β-amino acid residues from peptides. We determined the crystal structures of the native (αβ)₄ heterooctamer and of the 153 kDa precursor homotetramer at a resolution of 1.45 and 1.8 Å, respectively. These structures together with mutational analyses strongly support mechanisms for autoproteolysis and catalysis that involve residues Ser250, Ser288, and Glu290. The autoproteolytic mechanism is different from the one so far described for Ntn hydrolases. The structures together with functional data also provide insight into the discriminating features of the active site cleft that determine substrate specificity.


    Organizational Affiliation

    Biochemistry Institute, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-peptidyl aminopeptidaseA, B, C, D373Sphingosinicella xenopeptidilyticaMutation(s): 0 
Gene Names: bapA
EC: 3.4.11.25
Find proteins for Q52VH2 (Sphingosinicella xenopeptidilytica)
Explore Q52VH2 
Go to UniProtKB:  Q52VH2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.131 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.36α = 90
b = 96.72β = 108.23
c = 101.42γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-02-08
    Changes: Database references