7XS0

Trimer structure of HtrA from Helicobacter pylori bound with a tripeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures and solution conformations of HtrA from Helicobacter pylori reveal pH-dependent oligomeric conversion and conformational rearrangements.

Cui, L.Shi, X.Li, H.Wang, S.Guo, L.Lan, Z.Dai, Y.Zhang, Q.Wu, Y.Liu, W.

(2023) Int J Biol Macromol 243: 125274-125274

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.125274
  • Primary Citation of Related Structures:  
    7XS0, 7XS2

  • PubMed Abstract: 

    Helicobacter pylori is a Gram-negative microaerophilic bacterium that infects over 50 % of the world's population, making it a major risk factor for chronic gastritis, ulcer diseases of the stomach and duodenum, MALT lymphoma, and gastric cancer. The clinical consequences of H. pylori infection are closely linked with the expression of virulence factors secreted by the bacterium. One such virulence factor is high temperature requirement A (HtrA), which possesses chaperone and serine protease activity. In the host stomach, HtrA secreted from H. pylori (HpHtrA) disrupts intercellular adhesions by cleaving epithelial adhesion proteins including E-cadherin and desmoglein-2. This disruption causes intercellular junctions to open, allowing the bacterium to pass through the epithelial barrier, access the intercellular space, and colonize the gastric mucosa. HtrA proteases are well known for their structural complexity, reflected in their diverse oligomer forms and multi-tasking activities in both prokaryotes and eukaryotes. In this study, we determined crystal structures and solution conformations of HpHtrA monomer and trimer, which revealed large domain rearrangements between them. Notably, this is the first report of a monomeric structure in the HtrA family. We further found a pH-dependent dynamic trimer-to-monomer conversion and concurrent conformational changes that seem closely linked with a pH-sensing ability through the protonation of certain Asp residues. These results advance our understanding of the functional roles and the related mechanisms of this protease in bacterial infection, which may shed light on the development of HtrA-targeted therapies for H. pylori-associated diseases.


  • Organizational Affiliation

    Institute of Immunology, PLA, Army Medical University, Chongqing 400038, China; Department of Tropical Medicine and Infectious Diseases, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan 572000, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic serine endoprotease DegP-like441Helicobacter pylori 26695Mutation(s): 0 
Gene Names: HP_1019
EC: 3.4.21.107
UniProt
Find proteins for O25663 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25663 
Go to UniProtKB:  O25663
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25663
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-UNK-UNK3Escherichia coli BL21(DE3)Mutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.506α = 90
b = 139.506β = 90
c = 191.374γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-12-20
    Changes: Database references