5FZP | pdb_00005fzp

Structure of the dispase autolysis inducing protein from Streptomyces mobaraensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.191 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5FZP

This is version 1.4 of the entry. See complete history

Literature

Structure of the Dispase Autolysis Inducing Protein from Streptomyces Mobaraensis and Glutamine Cross-Linking Sites for Transglutaminase

Fiebig, D.Schmelz, S.Zindel, S.Ehret, V.Beck, J.Ebenig, A.Ehret, M.Froels, S.Pfeifer, F.Kolmar, H.Fuchsbauer, H.L.Scrima, A.

(2016) J Biological Chem 291: 20417

  • DOI: https://doi.org/10.1074/jbc.M116.731109
  • Primary Citation Related Structures: 
    5FZP

  • PubMed Abstract: 

    Transglutaminase from Streptomyces mobaraensis (MTG) is an important enzyme for cross-linking and modifying proteins. An intrinsic substrate of MTG is the dispase autolysis-inducing protein (DAIP). The amino acid sequence of DAIP contains 5 potential glutamines and 10 lysines for MTG-mediated cross-linking. The aim of the study was to determine the structure and glutamine cross-linking sites of the first physiological MTG substrate. A production procedure was established in Escherichia coli BL21 (DE3) to obtain high yields of recombinant DAIP. DAIP variants were prepared by replacing four of five glutamines for asparagines in various combinations via site-directed mutagenesis. Incorporation of biotin cadaverine revealed a preference of MTG for the DAIP glutamines in the order of Gln-39 ≫ Gln-298 > Gln-345 ∼ Gln-65 ≫ Gln-144. In the structure of DAIP the preferred glutamines do cluster at the top of the seven-bladed β-propeller. This suggests a targeted cross-linking of DAIP by MTG that may occur after self-assembly in the bacterial cell wall. Based on our biochemical and structural data of the first physiological MTG substrate, we further provide novel insight into determinants of MTG-mediated modification, specificity, and efficiency.


  • Organizational Affiliation
    • Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, 64287 Darmstadt, Germany, and the Department of Chemistry and.

Macromolecule Content 

  • Total Structure Weight: 73.18 kDa 
  • Atom Count: 6,026 
  • Modeled Residue Count: 685 
  • Deposited Residue Count: 696 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DISPASE AUTOLYSIS-INDUCING PROTEIN
A, B
348Streptomyces mobaraensisMutation(s): 0 
UniProt
Find proteins for P84908 (Streptomyces mobaraensis)
Explore P84908 
Go to UniProtKB:  P84908
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84908
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
L [auth B],
M [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.01α = 90
b = 101.13β = 90
c = 114.66γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-17
    Changes: Database references
  • Version 1.2: 2016-08-24
    Changes: Derived calculations
  • Version 1.3: 2016-10-05
    Changes: Database references
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary