5EZ1

Crystal Structure of Cell Binding Factor 2 from Helicobacter pylori in complex with I2CA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Helicobacter pylori cell binding factor 2: Insights into domain motion.

Naveen, V.Chu, C.H.Chen, B.W.Tsai, Y.C.Hsiao, C.D.Sun, Y.J.

(2016) J.Struct.Biol. 194: 90-101

  • DOI: 10.1016/j.jsb.2016.02.002

  • PubMed Abstract: 
  • Helicobacter pylori cell binding factor 2 (HpCBF2) is an antigenic virulence factor belonging to the SurA-like peptidyl-prolyl cis-trans isomerase family with implications for pathogenicity in the human gastrointestinal tract. HpCBF2 possesses PPIase ...

    Helicobacter pylori cell binding factor 2 (HpCBF2) is an antigenic virulence factor belonging to the SurA-like peptidyl-prolyl cis-trans isomerase family with implications for pathogenicity in the human gastrointestinal tract. HpCBF2 possesses PPIase activity and could act as a periplasmic chaperone to regulate outer membrane protein assembly. Here, we measured the isomerization and chaperone activity of HpCBF2, and determined the crystal structure of HpCBF2 in complex with an inhibitor, indole-2-carboxylic acid (I2CA), at 2.4Å resolution. HpCBF2-I2CA forms a homodimer encasing a large central hydrophobic cavity with a basket-like structure, and each monomer contains a PPIase and a chaperone domain. In the HpCBF2-I2CA dimer, the two PPIase domains separate by a distance of 22.8Å, while the two chaperone domains arrange in a domain-swap manner. The PPIase domains bound with I2CA ligand face towards the chaperone domains and are shielded by surrounding hydrophobic residues. With the aid of SAXS experiments, we also revealed domain motion between the apo- and I2CA-bound states of HpCBF2. The domain motion in HpCBF2 might be necessary for the isomerization activity of PPIase and the accommodation of the unfolded and partially folded peptides to refold by chaperone domain.


    Organizational Affiliation

    Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan. Electronic address: yjsun@life.nthu.edu.tw.,Molecular Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei 115, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.,Molecular Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei 115, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan. Electronic address: hsiao@gate.sinica.edu.tw.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative peptidyl-prolyl cis-trans isomerase HP_0175
A, B
277Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
EC: 5.2.1.8
Find proteins for P56112 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56112
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ICB
Query on ICB

Download SDF File 
Download CCD File 
A, B
1H-indole-2-carboxylic acid
C9 H7 N O2
HCUARRIEZVDMPT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 61.998α = 90.00
b = 61.998β = 90.00
c = 366.427γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release