5EZ1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

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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
  • Primary Citation of Related Structures:  
    5EZ1

  • 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 activity and could act as a periplasmic chaperone to regulate outer membrane protein assembly ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative peptidyl-prolyl cis-trans isomerase HP_0175A, B277Helicobacter pylori 26695Mutation(s): 0 
Gene Names: HP_0175
EC: 5.2.1.8
UniProt
Find proteins for P56112 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56112 
Go to UniProtKB:  P56112
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56112
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ICB
Query on ICB

Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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: 2.40 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.998α = 90
b = 61.998β = 90
c = 366.427γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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