5Y2D

Crystal structure of H. pylori HtrA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7001 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.331 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The unique trimeric assembly of the virulence factor HtrA fromHelicobacter pylorioccurs via N-terminal domain swapping.

Zhang, Z.Huang, Q.Tao, X.Song, G.Zheng, P.Li, H.Sun, H.Xia, W.

(2019) J.Biol.Chem. 294: 7990-8000

  • DOI: 10.1074/jbc.RA119.007387
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Knowledge of the molecular mechanisms of specific bacterial virulence factors can significantly contribute to antibacterial drug discovery. <i>Helicobacter pylori </i> is a Gram-negative microaerophilic bacterium that infects almost half of the worl ...

    Knowledge of the molecular mechanisms of specific bacterial virulence factors can significantly contribute to antibacterial drug discovery. Helicobacter pylori is a Gram-negative microaerophilic bacterium that infects almost half of the world's population, leading to gastric disorders and even gastric cancer. H. pylori expresses a series of virulence factors in the host, among which high-temperature requirement A ( Hp HtrA) is a newly identified serine protease secreted by H. pylori. Hp HtrA cleaves the extracellular domain of the epithelial cell surface adhesion protein E-cadherin and disrupts gastric epithelial cell junctions, allowing H. pylori to access the intercellular space. Here we report the first crystal structure of Hp HtrA at 3.0 Å resolution. The structure revealed a new type of HtrA protease trimer stabilized by unique N-terminal domain swapping distinct from other known HtrA homologs. We further observed that truncation of the N terminus completely abrogates Hp HtrA trimer formation as well as protease activity. In the presence of unfolded substrate, Hp HtrA assembled into cage-like 12-mers or 24-mers. Combining crystallographic, biochemical, and mutagenic data, we propose a mechanistic model of how Hp HtrA recognizes and cleaves the well-folded E-cadherin substrate. Our study provides a fundamental basis for the development of anti- H. pylori agents by using a previously uncharacterized HtrA protease as a target.


    Organizational Affiliation

    From the MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China.,From the MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China, xiawei5@mail.sysu.edu.cn.,the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,the Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong SAR, China, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic serine endoprotease DegP-like
A
465Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
EC: 3.4.21.107
Find proteins for G2J5T2 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  G2J5T2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UNK-UNK-UNK
B
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UNK-UNK-UNK-UNK-UNK
C
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
UNK-UNK-K-UNK-UNK-UNK-UNK-UNK-UNK-UNK
D
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
E
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
F
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7001 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.331 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 128.880α = 90.00
b = 128.880β = 90.00
c = 184.536γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-3000data reduction
PDB_EXTRACTdata extraction
PHENIXphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2019-08-28
    Type: Data collection, Database references