1L9N

Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions change structure for activation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions changes structure for activation.

Ahvazi, B.Kim, H.C.Kee, S.H.Nemes, Z.Steinert, P.M.

(2002) EMBO J. 21: 2055-2067

  • DOI: 10.1093/emboj/21.9.2055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transglutaminase (TGase) enzymes catalyze the formation of covalent cross-links between protein-bound glutamines and lysines in a calcium-dependent manner, but the role of Ca(2+) ions remains unclear. The TGase 3 isoform is widely expressed and is im ...

    Transglutaminase (TGase) enzymes catalyze the formation of covalent cross-links between protein-bound glutamines and lysines in a calcium-dependent manner, but the role of Ca(2+) ions remains unclear. The TGase 3 isoform is widely expressed and is important for epithelial barrier formation. It is a zymogen, requiring proteolysis for activity. We have solved the three-dimensional structures of the zymogen and the activated forms at 2.2 and 2.1 A resolution, respectively, and examined the role of Ca(2+) ions. The zymogen binds one ion tightly that cannot be exchanged. Upon proteolysis, the enzyme exothermally acquires two more Ca(2+) ions that activate the enzyme, are exchangeable and are functionally replaceable by other lanthanide trivalent cations. Binding of a Ca(2+) ion at one of these sites opens a channel which exposes the key Trp236 and Trp327 residues that control substrate access to the active site. Together, these biochemical and structural data reveal for the first time in a TGase enzyme that Ca(2+) ions induce structural changes which at least in part dictate activity and, moreover, may confer substrate specificity.


    Related Citations: 
    • Two non-proline cis peptide bonds may be important for factor XIII function
      Yee, V.C.,Pedersen, L.C.,Le Trong, I.,Bishop, P.D.,Stenkamp, R.E.,Teller, D.C.
      (1998) FEBS Lett. 423: 291
    • Three-dimensional structure of a transglutaminase: human blood coagulation factor XII
      Weiss, M.S.,Metzner, H.J.,Hilgenfeld, R.
      (1994) Proc.Natl.Acad.Sci.USA 91: 7296


    Organizational Affiliation

    Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892-8023, USA. Bijan@discus.niams.nih.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-glutamine glutamyltransferase E3
A, B
692Homo sapiensMutation(s): 1 
Gene Names: TGM3
EC: 2.3.2.13
Find proteins for Q08188 (Homo sapiens)
Go to Gene View: TGM3
Go to UniProtKB:  Q08188
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGL
Query on BGL

Download SDF File 
Download CCD File 
A, B
B-2-OCTYLGLUCOSIDE
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 57.488α = 93.23
b = 116.537β = 92.99
c = 60.768γ = 89.51
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2002-03-26 
  • Released Date: 2002-05-29 
  • Deposition Author(s): Ahvazi, B.

Revision History 

  • Version 1.0: 2002-05-29
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance