4PYG | pdb_00004pyg

Transglutaminase2 complexed with GTP

• PDB DOI: https://doi.org/10.2210/pdb4PYG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-27 Released: 2015-02-11 
• Deposition Author(s): Park, H.H., Jang, T.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.319 (Depositor), 0.309 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

Crystal structure of transglutaminase 2 with GTP complex and amino acid sequence evidence of evolution of GTP binding site.

Jang, T.H., Lee, D.S., Choi, K., Jeong, E.M., Kim, I.G., Kim, Y.W., Chun, J.N., Jeon, J.H., Park, H.H.

(2014) PLoS One 9: e107005-e107005

• PubMed: 25192068 
• DOI: https://doi.org/10.1371/journal.pone.0107005
• Primary Citation Related Structures: 
  4PYG


• PubMed Abstract: 
  

  Transglutaminase2 (TG2) is a multi-functional protein involved in various cellular processes, including apoptosis, differentiation, wound healing, and angiogenesis. The malfunction of TG2 causes many human disease including inflammatory disease, celiac disease, neurodegenerative diseases, tissue fibrosis, and cancers. Protein cross-linking activity, which is representative of TG2, is activated by calcium ions and suppressed by GTP. Here, we elucidated the structure of TG2 in complex with its endogenous inhibitor, GTP. Our structure showed why GTP is the optimal nucleotide for interacting with and inhibiting TG2. In addition, sequence comparison provided information describing the evolutionary scenario of GTP usage for controlling the activity of TG2.

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Organizational Affiliation: 
• School of Biotechnology, Yeungnam University, Gyeongsan, South Korea; Graduate School of Biochemistry, Yeungnam University, Gyeongsan, South Korea.
Department of Physiology and Biophysics at Seoul National University College of Medicine, Seoul, South Korea.
Department of Chemistry, Korea University, Seoul, South Korea.
Department of Biochemistry and Molecular Biology/Aging and Apoptosis Research Center (AARC), Seoul National University College of Medicine, Seoul, South Korea.
Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine and Lung Institute of Medical Research Center, Seoul National University College of Medicine, Seoul, South Korea.
Department of Physiology, Department of Biomedical Sciences, and Institute of Dermatological Science, Seoul National University College of Medicine, Seoul, South Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 237.02 kDa 
• Atom Count: 16,462 
• Modeled Residue Count: 2,055 
• Deposited Residue Count: 2,085 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-glutamine gamma-glutamyltransferase 2	A, B, C [auth E]	695	Homo sapiens	Mutation(s): 0  Gene Names: TGM2 EC: 2.3.2.13 (PDB Primary Data), 2.3.1 (UniProt), 3.4 (UniProt), 3.5.1.44 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P21980 (Homo sapiens) Explore P21980  Go to UniProtKB:  P21980
PHAROS:  P21980 GTEx:  ENSG00000198959

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	D [auth A], E [auth B], F [auth E]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.319 (Depositor), 0.309 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.546	α = 90
b = 216.218	β = 90
c = 165.183	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Park, H.H., Jang, T.H.

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary