1E9Z

Crystal structure of Helicobacter pylori urease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Supramolecular Assembly and Acid Resistance of Helicobacter Pylori Urease

Ha, N.-C.Oh, S.-T.Sung, J.Y.Cha, K.-A.Hyung Lee, M.Oh, B.-H.

(2001) Nat.Struct.Mol.Biol. 8: 480

  • DOI: 10.1038/88563
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Helicobacter pylori, an etiologic agent in a variety of gastroduodenal diseases, produces a large amount of urease, which is believed to neutralize gastric acid by producing ammonia for the survival of the bacteria. Up to 30% of the enzyme associates ...

    Helicobacter pylori, an etiologic agent in a variety of gastroduodenal diseases, produces a large amount of urease, which is believed to neutralize gastric acid by producing ammonia for the survival of the bacteria. Up to 30% of the enzyme associates with the surface of intact cells upon lysis of neighboring bacteria. The role of the enzyme at the extracellular location has been a subject of controversy because the purified enzyme is irreversibly inactivated below pH 5. We have determined the crystal structure of H. pylori urease, which has a 1.1 MDa spherical assembly of 12 catalytic units with an outer diameter of approximately 160 A. Under physiologically relevant conditions, the activity of the enzyme remains unaffected down to pH 3. Activity assays under different conditions indicated that the cluster of the 12 active sites on the supramolecular assembly may be critical for the survival of the enzyme at low pH. The structure provides a novel example of a molecular assembly adapted for acid resistance that, together with the low Km value of the enzyme, is likely to enable the organism to inhabit the hostile niche.


    Organizational Affiliation

    National Creative Research Initiative Center for Biomolecular Recognition, Department of Life Science and Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk, 790-784, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UREASE SUBUNIT ALPHA
A
238Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: ureA (hpuA)
EC: 3.5.1.5
Find proteins for P14916 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P14916
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UREASE SUBUNIT BETA
B
569Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: ureB (hpuB)
EC: 3.5.1.5
Find proteins for P69996 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P69996
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.212 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 177.910α = 90.00
b = 177.910β = 90.00
c = 177.910γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection