5WTL

Crystal structure of the periplasmic portion of outer membrane protein A (OmpA) from Capnocytophaga gingivalis

Summary for 5WTL

• Entry DOI: 10.2210/pdb5wtl/pdb
• Related: 5WTP
• Descriptor: OmpA family protein, CALCIUM ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: prokaryote, tt3r, tsp3, calcium-binding motif, membrane protein
• Biological source: Capnocytophaga gingivalis
• Total number of polymer chains: 4
• Total formula weight: 113938.35

Authors

Dai, S.,Tan, K.,Ye, S.,Zhang, R. (deposition date: 2016-12-13, release date: 2017-12-13, Last modification date: 2023-11-08)

Primary citation

Dai, S.,Sun, C.,Tan, K.,Ye, S.,Zhang, R.
Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability.
Cell Calcium, 66:78-89, 2017

PubMed Abstract: Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria. Here, we report the crystal structure of the periplasmic region of OmpA from Capnocytophaga gingivalis, which contains a linker region comprising five consecutive TT3Rs. The structure of OmpA-TT3R exhibits a well-ordered architecture organized around two tightly-coordinated Ca and confirms the presence of abnormal intra-repeat disulfide bonds. Further mutagenesis studies showed that the Ca-binding capability of OmpA-TT3R is indeed dependent on the proper formation of intra-repeat disulfide bonds, which help to fix a conserved glycine residue at its proper position for Ca coordination. Additionally, despite lacking inter-repeat disulfide bonds, the interfaces between adjacent OmpA-TT3Rs are enhanced by both hydrophobic and conserved aromatic-proline interactions.

PubMed: 28807152
DOI: 10.1016/j.ceca.2017.05.016

Experimental method

X-RAY DIFFRACTION (2.298 Å)