1G0D

CRYSTAL STRUCTURE OF RED SEA BREAM TRANSGLUTAMINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of red sea bream transglutaminase.

Noguchi, K.Ishikawa, K.Yokoyama, K.i.Ohtsuka, T.Nio, N.Suzuki, E.

(2001) J.Biol.Chem. 276: 12055-12059

  • DOI: 10.1074/jbc.M009862200

  • PubMed Abstract: 
  • The crystal structure of the tissue-type transglutaminase from red sea bream liver (fish-derived transglutaminase, FTG) has been determined at 2.5-A resolution using the molecular replacement method, based on the crystal structure of human blood coag ...

    The crystal structure of the tissue-type transglutaminase from red sea bream liver (fish-derived transglutaminase, FTG) has been determined at 2.5-A resolution using the molecular replacement method, based on the crystal structure of human blood coagulation factor XIII, which is a transglutaminase zymogen. The model contains 666 residues of a total of 695 residues, 382 water molecules, and 1 sulfate ion. FTG consists of four domains, and its overall and active site structures are similar to those of human factor XIII. However, significant structural differences are observed in both the acyl donor and acyl acceptor binding sites, which account for the difference in substrate preferences. The active site of the enzyme is inaccessible to the solvent, because the catalytic Cys-272 hydrogen-bonds to Tyr-515, which is thought to be displaced upon acyl donor binding to FTG. It is postulated that the binding of an inappropriate substrate to FTG would lead to inactivation of the enzyme because of the formation of a new disulfide bridge between Cys-272 and the adjacent Cys-333 immediately after the displacement of Tyr-515. Considering the mutational studies previously reported on the tissue-type transglutaminases, we propose that Cys-333 and Tyr-515 are important in strictly controlling the enzymatic activity of FTG.


    Related Citations: 
    • Tissue-type transglutaminase from red sea bream (Pagrus major)
      Yasueda, H.,Nakanishi, K.,Kumazawa, Y.,Nagase, K.,Motoki, M.,Matsui, H.
      (1995) Eur.J.Biochem. 232: 411
    • Overproduction of DnaJ in Escherichia coli Improves in Vivo Solubility of the Recombinant Fish-derived Transglutaminase
      Yokoyama, K.,Kikuchi, Y.,Yasueda, H.
      (1998) Biosci.Biotechnol.Biochem. 62: 1205


    Organizational Affiliation

    Central Research Laboratories and Food Research & Development Laboratories, Ajinomoto Company Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, Kanagawa 210-8681, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE
A
695Pagrus majorMutation(s): 0 
Gene Names: tgl2
EC: 2.3.2.13
Find proteins for P52181 (Pagrus major)
Go to UniProtKB:  P52181
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 97.800α = 90.00
b = 97.800β = 90.00
c = 455.500γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance