1NUG

Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 calciums, 1 Mg, inactive form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Roles of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme

Ahvazi, B.Boeshans, K.M.Idler, W.Baxa, U.Steinert, P.M.

(2003) J.Biol.Chem. 278: 23834-23841

  • DOI: 10.1074/jbc.M301162200
  • Primary Citation of Related Structures:  1NUD, 1NUF

  • PubMed Abstract: 
  • The transglutaminase 3 enzyme is widely expressed in many tissues including epithelia. We have shown previously that it can bind three Ca2+ ions, which in site one is constitutively bound, while those in sites two and three are acquired during activa ...

    The transglutaminase 3 enzyme is widely expressed in many tissues including epithelia. We have shown previously that it can bind three Ca2+ ions, which in site one is constitutively bound, while those in sites two and three are acquired during activation and are required for activity. In particular, binding at site three opens a channel through the enzyme and exposes two tryptophan residues near the active site that are thought to be important for enzyme reaction. In this study, we have solved the structures of three more forms of this enzyme by x-ray crystallography in the presence of Ca2+ and/or Mg2+, which provide new insights on the precise contribution of each Ca2+ ion to activation and activity. First, we found that Ca2+ ion in site one can be exchanged with difficulty, and it has a binding affinity of Kd = 0.3 microm (DeltaH = -6.70 +/- 0.52 kcal/mol), which suggests it is important for the stabilization of the enzyme. Site two can be occupied by some lanthanides but only Ca2+ of the Group 2 family of alkali earth metals, and its occupancy are required for activity. Site three can be occupied by some lanthanides, Ca2+,or Mg2+; however, when Mg2+ is present, the enzyme is inactive, and the channel is closed. Thus Ca2+ binding in both sites two and three cooperate in opening the channel. We speculate that manipulation of the channel opening could be controlled by intracellular cation levels. Together, these data have important implications for reaction mechanism of the enzyme: the opening of a channel perhaps controls access to and manipulation of substrates at the active site.


    Related Citations: 
    • 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
    • Crystallization and Preliminary X-ray Analysis of Human Transglutaminase 3 from Zymogen to Active Form
      Kim, H.C.,Nemes, Z.,Idler, W.W.,Hyde, C.C.,Steinert, P.M.,Ahvazi, B.
      (2001) J.Struct.Biol. 135: 73


    Organizational Affiliation

    Laboratory of Skin Biology, the Laboratory of X-ray Crystallography/Office of Science and Technology, National Institute of Health, Bethesda, Maryland 20892-8023, USA. Bijan@discus.niams.nih.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-glutamine glutamyltransferase E
A, B
692Homo sapiensGene 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
CL
Query on CL

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

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.194 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 57.510α = 97.24
b = 66.810β = 90.28
c = 116.530γ = 98.36
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2003-01-31 
  • Released Date: 2003-04-22 
  • Deposition Author(s): Ahvazi, B.

Revision History 

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance