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PDBsum entry 1g0d

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protein ligands links
Transferase PDB id
1g0d
Jmol
Contents
Protein chain
666 a.a. *
Ligands
SO4
Waters ×383
* Residue conservation analysis
PDB id:
1g0d
Name: Transferase
Title: Crystal structure of red sea bream transglutaminase
Structure: Protein-glutamine gamma-glutamyltransferase. Chain: a. Engineered: yes
Source: Pagrus major. Red seabream. Organism_taxid: 143350. Tissue: liver. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.200     R-free:   0.249
Authors: K.Noguchi,K.Ishikawa,K.Yokoyama,T.Ohtsuka,N.Nio,E.Suzuki
Key ref:
K.Noguchi et al. (2001). Crystal structure of red sea bream transglutaminase. J Biol Chem, 276, 12055-12059. PubMed id: 11080504 DOI: 10.1074/jbc.M009862200
Date:
06-Oct-00     Release date:   23-May-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P52181  (TGM2_PAGMA) -  Protein-glutamine gamma-glutamyltransferase 2
Seq:
Struc:
 
Seq:
Struc:
695 a.a.
666 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.2.13  - Protein-glutamine gamma-glutamyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein glutamine + alkylamine = protein N5-alkylglutamine + NH3
Protein glutamine
+ alkylamine
= protein N(5)-alkylglutamine
+ NH(3)
      Cofactor: Ca(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     peptide cross-linking   1 term 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M009862200 J Biol Chem 276:12055-12059 (2001)
PubMed id: 11080504  
 
 
Crystal structure of red sea bream transglutaminase.
K.Noguchi, K.Ishikawa, Yokoyama Ki, T.Ohtsuka, N.Nio, E.Suzuki.
 
  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 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.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Schematic ribbon drawings of FTG (left) and human factor XIII (right). Helices and sheets are colored red and blue, respectively. Both TGases consist of four domains: -sandwich, core, barrel 1, and barrel 2 from the N terminus. Human factor XIII has an activation peptide (green) at the N terminus. The active site in each TGase is marked with a yellow asterisk. This figure was produced using MOLSCRIPT (36).
Figure 2.
Fig. 2. Structural comparison of FTG with human factor XIII. Stereoviews of the C traces of FTG and human factor XIII are shown. The superposition was done using QUANTA97. FTG, human factor XIII, and the activation peptide are colored blue, red, and green, respectively. The active site in each TGase is marked with a white asterisk.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 12055-12059) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23151626 S.S.Bhaskaran, and C.E.Stebbins (2012).
Structure of the catalytic domain of the Salmonella virulence factor SseI.
  Acta Crystallogr D Biol Crystallogr, 68, 1613-1621.
PDB codes: 4g29 4g2b
20722598 B.A.Wilson, and M.Ho (2010).
Recent insights into Pasteurella multocida toxin and other G-protein-modulating bacterial toxins.
  Future Microbiol, 5, 1185-1201.  
20195702 H.Kumeta, N.Miwa, K.Ogura, Y.Kai, T.Mizukoshi, N.Shimba, E.Suzuki, and F.Inagaki (2010).
The NMR structure of protein-glutaminase from Chryseobacterium proteolyticum.
  J Biomol NMR, 46, 251-255.
PDB code: 2ksv
19850674 U.Tagami, N.Shimba, M.Nakamura, K.Yokoyama, E.Suzuki, and T.Hirokawa (2009).
Substrate specificity of microbial transglutaminase as revealed by three-dimensional docking simulation and mutagenesis.
  Protein Eng Des Sel, 22, 747-752.  
18092889 D.M.Pinkas, P.Strop, A.T.Brunger, and C.Khosla (2007).
Transglutaminase 2 undergoes a large conformational change upon activation.
  PLoS Biol, 5, e327.
PDB code: 2q3z
17179049 G.E.Begg, L.Carrington, P.H.Stokes, J.M.Matthews, M.A.Wouters, A.Husain, L.Lorand, S.E.Iismaa, and R.M.Graham (2006).
Mechanism of allosteric regulation of transglutaminase 2 by GTP.
  Proc Natl Acad Sci U S A, 103, 19683-19688.  
15010546 R.A.Chica, P.Gagnon, J.W.Keillor, and J.N.Pelletier (2004).
Tissue transglutaminase acylation: Proposed role of conserved active site Tyr and Trp residues revealed by molecular modeling of peptide substrate binding.
  Protein Sci, 13, 979-991.  
12535215 A.Kon, H.Takeda, H.Sasaki, K.Yoneda, K.Nomura, B.Ahvazi, P.M.Steinert, K.Hanada, and I.Hashimoto (2003).
Novel transglutaminase 1 gene mutations (R348X/Y365D) in a Japanese family with lamellar ichthyosis.
  J Invest Dermatol, 120, 170-172.  
12563291 L.Lorand, and R.M.Graham (2003).
Transglutaminases: crosslinking enzymes with pleiotropic functions.
  Nat Rev Mol Cell Biol, 4, 140-156.  
12732581 M.Date, K.Yokoyama, Y.Umezawa, H.Matsui, and Y.Kikuchi (2003).
Production of native-type Streptoverticillium mobaraense transglutaminase in Corynebacterium glutamicum.
  Appl Environ Microbiol, 69, 3011-3014.  
14566064 S.E.Iismaa, S.Holman, M.A.Wouters, L.Lorand, R.M.Graham, and A.Husain (2003).
Evolutionary specialization of a tryptophan indole group for transition-state stabilization by eukaryotic transglutaminases.
  Proc Natl Acad Sci U S A, 100, 12636-12641.  
12514016 Y.Kikuchi, M.Date, K.Yokoyama, Y.Umezawa, and H.Matsui (2003).
Secretion of active-form Streptoverticillium mobaraense transglutaminase by Corynebacterium glutamicum: processing of the pro-transglutaminase by a cosecreted subtilisin-Like protease from Streptomyces albogriseolus.
  Appl Environ Microbiol, 69, 358-366.  
11980702 B.Ahvazi, H.C.Kim, S.H.Kee, Z.Nemes, and P.M.Steinert (2002).
Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions changes structure for activation.
  EMBO J, 21, 2055-2067.
PDB codes: 1l9m 1l9n
12485989 F.Brunner, S.Rosahl, J.Lee, J.J.Rudd, C.Geiler, S.Kauppinen, G.Rasmussen, D.Scheel, and T.Nürnberger (2002).
Pep-13, a plant defense-inducing pathogen-associated pattern from Phytophthora transglutaminases.
  EMBO J, 21, 6681-6688.  
12368090 L.Fesus, and M.Piacentini (2002).
Transglutaminase 2: an enigmatic enzyme with diverse functions.
  Trends Biochem Sci, 27, 534-539.  
11867764 S.N.Murthy, S.Iismaa, G.Begg, D.M.Freymann, R.M.Graham, and L.Lorand (2002).
Conserved tryptophan in the core domain of transglutaminase is essential for catalytic activity.
  Proc Natl Acad Sci U S A, 99, 2738-2742.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.