5EZ1

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

Summary for 5EZ1

• Entry DOI: 10.2210/pdb5ez1/pdb
• Descriptor: Putative peptidyl-prolyl cis-trans isomerase HP_0175, 1H-indole-2-carboxylic acid (3 entities in total)
• Functional Keywords: cell binding factor 2, peptidyl prolyl cis-trans isomerase, isomerase
• Biological source: Helicobacter pylori (strain ATCC 700392 / 26695)
• Total number of polymer chains: 2
• Total formula weight: 64261.39

Authors

Sun, Y.J.,Chu, C.H.,Tsai, Y.C. (deposition date: 2015-11-26, release date: 2016-03-16, Last modification date: 2024-03-20)

Primary citation

Naveen, V.,Chu, C.H.,Chen, B.W.,Tsai, Y.C.,Hsiao, C.D.,Sun, Y.J.
Helicobacter pylori cell binding factor 2: Insights into domain motion.
J.Struct.Biol., 194:90-101, 2016

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. 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.

PubMed: 26850168
DOI: 10.1016/j.jsb.2016.02.002

Experimental method

X-RAY DIFFRACTION (2.4 Å)