3WOR

Crystal structure of the DAP BII octapeptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

S46 peptidases are the first exopeptidases to be members of clan PA

Sakamoto, Y.Suzuki, Y.Iizuka, I.Tateoka, C.Roppongi, S.Fujimoto, M.Inaka, K.Tanaka, H.Masaki, M.Ohta, K.Okada, H.Nonaka, T.Morikawa, Y.Nakamura, K.T.Ogasawara, W.Tanaka, N.

(2014) SCI REP 4: 4977-4977

  • DOI: 10.1038/srep04977
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The dipeptidyl aminopeptidase BII (DAP BII) belongs to a serine peptidase family, S46. The amino acid sequence of the catalytic unit of DAP BII exhibits significant similarity to those of clan PA endopeptidases, such as chymotrypsin. However, the mol ...

    The dipeptidyl aminopeptidase BII (DAP BII) belongs to a serine peptidase family, S46. The amino acid sequence of the catalytic unit of DAP BII exhibits significant similarity to those of clan PA endopeptidases, such as chymotrypsin. However, the molecular mechanism of the exopeptidase activity of family S46 peptidase is unknown. Here, we report crystal structures of DAP BII. DAP BII contains a peptidase domain including a typical double β-barrel fold and previously unreported α-helical domain. The structures of peptide complexes revealed that the α-helical domain covers the active-site cleft and the side chain of Asn330 in the domain forms hydrogen bonds with the N-terminus of the bound peptide. These observations indicate that the α-helical domain regulates the exopeptidase activity of DAP BII. Because S46 peptidases are not found in mammals, we expect that our study will be useful for the design of specific inhibitors of S46 peptidases from pathogens.


    Organizational Affiliation

    1] School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, JAPAN [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
dipeptidyl aminopeptidase BII
A, B
698Pseudoxanthomonas mexicanaMutation(s): 3 
Gene Names: dapb2
EC: 3.4.14.-
Find proteins for V5YM14 (Pseudoxanthomonas mexicana)
Go to UniProtKB:  V5YM14
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Angiotensin II
C, D
8Homo sapiensMutation(s): 0 
Gene Names: AGT (SERPINA8)
Find proteins for P01019 (Homo sapiens)
Go to Gene View: AGT
Go to UniProtKB:  P01019
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.166 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 122.008α = 90.00
b = 122.008β = 90.00
c = 219.157γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release