4ZG0

Crystal structure of Mouse Syndesmos protein

Summary for 4ZG0

• Entry DOI: 10.2210/pdb4zg0/pdb
• Descriptor: Protein syndesmos (2 entities in total)
• Functional Keywords: nudix hydrolase, cytoplasmic protein, syndecan-4 cytoplasmic domain interactor, hydrolase
• Biological source: Mus musculus (Mouse)
• Cellular location: Cytoplasm : Q8VHN8
• Total number of polymer chains: 2
• Total formula weight: 47004.52

Authors

Lee, I.,Kim, H.,Yoo, J.,Cho, H.,Lee, W. (deposition date: 2015-04-22, release date: 2016-04-20, Last modification date: 2023-11-08)

Primary citation

Kim, H.,Yoo, J.,Lee, I.,Kang, Y.J.,Cho, H.S.,Lee, W.
Crystal structure of syndesmos and its interaction with Syndecan-4 proteoglycan
Biochem.Biophys.Res.Commun., 463:762-767, 2015

PubMed Abstract: Syndesmos, nucleoside diphosphate linked moiety X (nudix)-type motif 16-like 1 (Nudt16l1), is evolutionarily divergent from the Nudt16 family. Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain (Syn4(cyto)) in focal contacts, interacts with various cell adhesion adaptor proteins to control cell signaling. We determined the X-ray crystal structure of syndesmos; it is composed of seven α-helices and seven β-strands. Although syndesmos has a molecular topology similar to that of nudix hydrolase proteins, the structure of the nudix motif differs from that of X29. The dimeric interface of syndesmos is composed of α-helix 4, 7 and β-strand 2, 7, which primarily form hydrophobic interactions. The binding interaction between syndesmos and syn4(cyto) was characterized as a low-affinity interaction (Kd = 62 μM) by surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR). The NMR resonances of Lys (177, 178, 179), Gly182, and Ser183 in the C1 region and Lys193 and Lys194 in the V region of syndecan-4 are perturbed upon syndesmos binding. Our results provide structural insight into the molecular function of syndesmos in the regulation of cell signaling via binding to syndecan-4.

PubMed: 26100207
DOI: 10.1016/j.bbrc.2015.06.010

Experimental method

X-RAY DIFFRACTION (2.006 Å)