3GIO | pdb_00003gio

Crystal structure of the TNF-alpha inducing protein (Tip alpha) from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb3GIO/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-05 Released: 2009-08-04 
• Deposition Author(s): Jang, J.Y., Yoon, H.J., Yoon, J.Y., Kim, H.S., Lee, S.J., Kim, K.H., Kim, D.J., Han, B.G., Lee, B.I., Jang, S., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.233 (DCC) 

Literature

Crystal Structure of the TNF-alpha-Inducing Protein (Tipalpha) from Helicobacter pylori: Insights into Its DNA-Binding Activity.

Jang, J.Y., Yoon, H.J., Yoon, J.Y., Kim, H.S., Lee, S.J., Kim, K.H., Kim, D.J., Jang, S., Han, B.G., Lee, B.I., Suh, S.W.

(2009) J Mol Biology 

• PubMed: 19596016 
• DOI: https://doi.org/10.1016/j.jmb.2009.07.010
• Primary Citation Related Structures: 
  3GIO


• PubMed Abstract: 
  

  Helicobacter pylori infection is one of the highest risk factors for gastroduodenal diseases including gastric cancer. Tumor necrosis factor-alpha (TNF-alpha) is one of the essential cytokines for tumor promotion, and thus, an H. pylori protein that induces TNF-alpha is believed to play a significant role in gastric cancer development in humans. The HP0596 gene product of H. pylori strain 26695 was identified as the TNF-alpha-inducing protein (Tipalpha). Tipalpha is secreted from H. pylori as dimers and enters the gastric cells. It was shown to have a DNA-binding activity. Here, we have determined the crystal structure of Tipalpha from H. pylori. Its monomer consists of two structural domains ("mixed domain" and "helical domain"). Tipalpha exists as a dimer in the crystal, and the dimeric structure represents a novel scaffold for DNA binding. A positively charged surface patch formed across the two monomers of the Tipalpha dimer by the loop between helices alpha1 and alpha2 may be important in DNA binding.

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Organizational Affiliation: 
• Department of Chemistry, Seoul National University, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 42.91 kDa 
• Atom Count: 2,460 
• Modeled Residue Count: 296 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	186	Helicobacter pylori	Mutation(s): 0  Gene Names: HP_0596
UniProt
Find proteins for O25318 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25318  Go to UniProtKB:  O25318

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.233 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.519	α = 90
b = 67.114	β = 90
c = 91.263	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Jang, J.Y., Yoon, H.J., Yoon, J.Y., Kim, H.S., Lee, S.J., Kim, K.H., Kim, D.J., Han, B.G., Lee, B.I., Jang, S., Suh, S.W.

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary