3N33

Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with pefabloc SC (AEBSF)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.str.2012.07.017
  • Primary Citation of Related Structures:  
    3N2W, 3N33, 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 1.45 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-peptidyl aminopeptidase
A, B, C, D
373Sphingosinicella xenopeptidilyticaMutation(s): 0 
Gene Names: bapA
EC: 3.4.11.25
UniProt
Find proteins for Q52VH2 (Sphingosinicella xenopeptidilytica)
Explore Q52VH2 
Go to UniProtKB:  Q52VH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ52VH2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
F [auth A],
O [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
AES
Query on AES

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
G [auth A]
H [auth A]
P [auth B]
DA [auth D],
EA [auth D],
G [auth A],
H [auth A],
P [auth B],
Q [auth B],
V [auth C],
W [auth C]
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
C8 H10 F N O2 S
MGSKVZWGBWPBTF-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
FA [auth D]
GA [auth D]
HA [auth D]
AA [auth C],
BA [auth C],
FA [auth D],
GA [auth D],
HA [auth D],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth B],
S [auth B],
T [auth B],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth D],
E [auth A],
N [auth B],
U [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.4α = 90
b = 96.85β = 108.38
c = 101.3γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description