4Y3K

Structure of Vaspin mutant E379S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

A unique serpin P1' glutamate and a conserved beta-sheet C arginine are key residues for activity, protease recognition and stability of serpinA12 (vaspin).

Ulbricht, D.Pippel, J.Schultz, S.Meier, R.Strater, N.Heiker, J.T.

(2015) Biochem.J. 470: 357-367

  • DOI: 10.1042/BJ20150643
  • Primary Citation of Related Structures:  
  • Also Cited By: 5EI0

  • PubMed Abstract: 
  • SerpinA12 (vaspin) is thought to be mainly expressed in adipose tissue and has multiple beneficial effects on metabolic, inflammatory and atherogenic processes related to obesity. KLK7 (kallikrein 7) is the only known protease target of vaspin to dat ...

    SerpinA12 (vaspin) is thought to be mainly expressed in adipose tissue and has multiple beneficial effects on metabolic, inflammatory and atherogenic processes related to obesity. KLK7 (kallikrein 7) is the only known protease target of vaspin to date and is inhibited with a moderate inhibition rate. In the crystal structure, the cleavage site (P1-P1') of the vaspin reactive centre loop is fairly rigid compared with the flexible residues before P2, possibly supported by an ionic interaction of P1' glutamate (Glu(379)) with an arginine residue (Arg(302)) of the β-sheet C. A P1' glutamate seems highly unusual and unfavourable for the protease KLK7. We characterized vaspin mutants to investigate the roles of these two residues in protease inhibition and recognition by vaspin. Reactive centre loop mutations changing the P1' residue or altering the reactive centre loop conformation significantly increased inhibition parameters, whereas removal of the positive charge within β-sheet C impeded the serpin-protease interaction. Arg(302) is a crucial contact to enable vaspin recognition by KLK7 and it supports moderate inhibition of the serpin despite the presence of the detrimental P1' Glu(379), which clearly represents a major limiting factor for vaspin-inhibitory activity. We also show that the vaspin-inhibition rate for KLK7 can be modestly increased by heparin and demonstrate that vaspin is a heparin-binding serpin. Noteworthily, we observed vaspin as a remarkably thermostable serpin and found that Glu(379) and Arg(302) influence heat-induced polymerization. These structural and functional results reveal the mechanistic basis of how reactive centre loop sequence and exosite interaction in vaspin enable KLK7 recognition and regulate protease inhibition as well as stability of this adipose tissue-derived serpin.


    Organizational Affiliation

    Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, 04103 Leipzig, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serpin A12
A, B
414Homo sapiensMutation(s): 1 
Gene Names: SERPINA12
Find proteins for Q8IW75 (Homo sapiens)
Go to Gene View: SERPINA12
Go to UniProtKB:  Q8IW75
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 132.959α = 90.00
b = 151.353β = 98.43
c = 61.602γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACphasing
BUSTERrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB1052 C4, C7
European UnionGermany100121469

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Database references
  • Version 2.0: 2017-09-06
    Type: Atomic model, Author supporting evidence, Derived calculations