Crystal structure of syndesmos and its interaction with Syndecan-4 proteoglycan

Heeyoun Kim, Jiho Yoo, Inhwan Lee, Ying Jin Kang, Hyun Soo Cho, Weontae Lee

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5 Citations (Scopus)


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 (Syn4cyto) 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 syn4cyto 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.

Original languageEnglish
Pages (from-to)762-767
Number of pages6
JournalBiochemical and Biophysical Research Communications
Issue number4
Publication statusPublished - 2015 Jul 13

Bibliographical note

Funding Information:
This work was supported by the Translational Research Center for Protein Function Control ( 2009-0083522 ) and the Mid-career Researcher Program ( NRF-2013R1A2A2A01068963 to WL) from the Ministry of Future Creation and Science (MFCS) of Korea. Authors thank for technical assistance provided at Beamline 5C (4A) and 7A of the Pohang Light Source and Beamline 1A of the Photon Factory.

Publisher Copyright:
© 2015 Elsevier Inc. All rights reserved.

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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