2D2R | pdb_00002d2r

Crystal structure of Helicobacter pylori Undecaprenyl Pyrophosphate Synthase

• PDB DOI: https://doi.org/10.2210/pdb2D2R/pdb

• Classification: TRANSFERASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-16 Released: 2006-09-26 
• Deposition Author(s): Kuo, C.J., Guo, R.T., Chen, C.L., Ko, T.P., Cheng, Y.S., Cheng, Y.L., Liang, P.H., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.240 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

Structure-based inhibitors exhibit differential activities against Helicobacter pylori and Escherichia coli undecaprenyl pyrophosphate synthases.

Kuo, C.J., Guo, R.T., Lu, I.L., Liu, H.G., Wu, S.Y., Ko, T.P., Wang, A.H., Liang, P.H.

(2008) J Biomed Biotechnol 2008: 841312-841312

• PubMed: 18382620 
• DOI: https://doi.org/10.1155/2008/841312
• Primary Citation of Related Structures:  
  2D2R


• PubMed Abstract: 
  

  Helicobacter pylori colonizes the human gastric epithelium and causes diseases such as gastritis, peptic ulcers, and stomach cancer. Undecaprenyl pyrophosphate synthase (UPPS), which catalyzes consecutive condensation reactions of farnesyl pyrophosphate with eight isopentenyl pyrophosphate to form lipid carrier for bacterial peptidoglycan biosynthesis, represents a potential target for developing new antibiotics. In this study, we solved the crystal structure of H. pylori UPPS and performed virtual screening of inhibitors from a library of 58,635 compounds. Two hits were found to exhibit differential activities against Helicobacter pylori and Escherichia coli UPPS, giving the possibility of developing antibiotics specially targeting pathogenic H. pylori without killing the intestinal E. coli.

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Organizational Affiliation: 

Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan.

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: 57.15 kDa 
• Atom Count: 4,035 
• Modeled Residue Count: 418 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Undecaprenyl Pyrophosphate Synthase	A, B	245	Helicobacter pylori	Mutation(s): 0  EC: 2.5.1.31 (PDB Primary Data), 2.5.1 (UniProt)
UniProt
Find proteins for P55984 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P55984  Go to UniProtKB:  P55984

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.240 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.240 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.63	α = 90
b = 58.914	β = 90
c = 153.425	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-26 
Deposition Author(s): Kuo, C.J., Guo, R.T., Chen, C.L., Ko, T.P., Cheng, Y.S., Cheng, Y.L., Liang, P.H., Wang, A.H.-J.

Revision History  

• Version 1.0: 2006-09-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description