4BBK

Structural and functional characterisation of the kindlin-1 pleckstrin homology domain

Summary for 4BBK

• Entry DOI: 10.2210/pdb4bbk/pdb
• Descriptor: FERMITIN FAMILY HOMOLOG 1, GLYCEROL (3 entities in total)
• Functional Keywords: ph domain, cell adhesion
• Biological source: MUS MUSCULUS (HOUSE MOUSE)
• Total number of polymer chains: 1
• Total formula weight: 18961.03

Authors

Yates, L.A.,Lumb, C.N.,Brahme, N.N.,Zalyte, R.,Bird, L.E.,De Colibus, L.,Owens, R.J.,Calderwood, D.A.,Sansom, M.S.P.,Gilbert, R.J.C. (deposition date: 2012-09-25, release date: 2012-11-14, Last modification date: 2023-12-20)

Primary citation

Yates, L.A.,Lumb, C.N.,Brahme, N.N.,Zalyte, R.,Bird, L.E.,De Colibus, L.,Owens, R.J.,Calderwood, D.A.,Sansom, M.S.P.,Gilbert, R.J.C.
Structural and Functional Characterisation of the Kindlin-1 Pleckstrin Homology Domain
J.Biol.Chem., 287:43246-, 2012

PubMed Abstract: Inside-out activation of integrins is mediated via the binding of talin and kindlin to integrin β-subunit cytoplasmic tails. The kindlin FERM domain is interrupted by a pleckstrin homology (PH) domain within its F2 subdomain. Here, we present data confirming the importance of the kindlin-1 PH domain for integrin activation and its x-ray crystal structure at a resolution of 2.1 Å revealing a C-terminal second α-helix integral to the domain but found only in the kindlin protein family. An isoform-specific salt bridge occludes the canonical phosphoinositide binding site, but molecular dynamics simulations display transient switching to an alternative open conformer. Molecular docking reveals that the opening of the pocket would enable potential ligands to bind within it. Although lipid overlay assays suggested the PH domain binds inositol monophosphates, surface plasmon resonance demonstrated weak affinities for inositol 3,4,5-triphosphate (Ins(3,4,5)P(3); K(D) ∼100 μM) and no monophosphate binding. Removing the salt bridge by site-directed mutagenesis increases the PH domain affinity for Ins(3,4,5)P(3) as measured by surface plasmon resonance and enables it to bind PtdIns(3,5)P(2) on a dot-blot. Structural comparison with other PH domains suggests that the phosphate binding pocket in the kindlin-1 PH domain is more occluded than in kindlins-2 and -3 due to its salt bridge. In addition, the apparent affinity for Ins(3,4,5)P(3) is affected by the presence of PO(4) ions in the buffer. We suggest the physiological ligand of the kindlin-1 PH domain is most likely not an inositol phosphate but another phosphorylated species.

PubMed: 23132860
DOI: 10.1074/JBC.M112.422089

Experimental method

X-RAY DIFFRACTION (2.1 Å)