5X6T

N-terminal Zinc Finger of Synaptotagmin-like Protein 4

Summary for 5X6T

• Entry DOI: 10.2210/pdb5x6t/pdb
• NMR Information: BMRB: 36062
• Descriptor: Synaptotagmin-like protein 4, ZINC ION (2 entities in total)
• Functional Keywords: synaptotagmin, metal binding protein
• Biological source: Homo sapiens (Human)
• Cellular location: Membrane ; Peripheral membrane protein : Q96C24
• Total number of polymer chains: 1
• Total formula weight: 6171.78

Authors

Miyamoto, K. (deposition date: 2017-02-23, release date: 2017-10-11, Last modification date: 2024-05-15)

Primary citation

Miyamoto, K.,Nakatani, A.,Saito, K.
The unique N-terminal zinc finger of synaptotagmin-like protein 4 reveals FYVE structure
Protein Sci., 26:2451-2457, 2017

PubMed Abstract: Synaptotagmin-like protein 4 (Slp4), expressed in human platelets, is associated with dense granule release. Slp4 is comprised of the N-terminal zinc finger, Slp homology domain, and C2 domains. We synthesized a compact construct (the Slp4N peptide) corresponding to the Slp4 N-terminal zinc finger. Herein, we have determined the solution structure of the Slp4N peptide by nuclear magnetic resonance (NMR). Furthermore, experimental, chemical modification of Cys residues revealed that the Slp4N peptide binds two zinc atoms to mediate proper folding. NMR data showed that eight Cys residues coordinate zinc atoms in a cross-brace fashion. The Simple Modular Architecture Research Tool database predicted the structure of Slp4N as a RING finger. However, the actual structure of the Slp4N peptide adopts a unique C C -type FYVE fold and is distinct from a RING fold. To create an artificial RING finger (ARF) with specific ubiquitin-conjugating enzyme (E2)-binding capability, cross-brace structures with eight zinc-ligating residues are needed as the scaffold. The cross-brace structure of the Slp4N peptide could be utilized as the scaffold for the design of ARFs.

PubMed: 28906046
DOI: 10.1002/pro.3301

Experimental method

SOLUTION NMR