The NMR structure of the murine DLC2 SAM domain reveals a variant fold that is similar to a four-helix bundle

Department of Biology, York University, Toronto, Ontario, Canada. <>
BMC Structural Biology (Impact Factor: 1.18). 02/2007; 7(1):34. DOI: 10.1186/1472-6807-7-34
Source: PubMed


The tumor suppressor DLC2 (Deleted in Liver Cancer -2) participates in cell signaling at the mitochondrial membrane. DLC2 is characterized by a SAM (sterile alpha motif) domain, a Rho GTPase activating protein (GAP) domain, and a START lipid transfer domain.
Towards understanding the function of DLC2, we have solved the NMR solution structure of the SAM domain. The DLC2-SAM domain structure reveals an atypical four-helix composition that is distinct from the five-helix SAM domain structures that have been determined to date. From structural alignments, helix 3 of the canonical SAM domain appears to be replaced by shorter, extended secondary structure that follows a similar path. Another difference is demonstrated by helices 1 and 2 that form a helical hairpin that is situated approximately parallel to the canonical helix 5.
The DLC2-SAM domain adopts a structure that is topologically more similar to an anti-parallel four-helix bundle than a canonical SAM domain. This alternate topology may allow the DLC2-SAM domain to interact with a novel set of ligands.

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    • "Several studies suggest that the principal role of SAM domains is to mediate protein-protein and protein-nucleic acid interactions (Kim et al., 2002; Lackmann et al., 1998; Ramachander and Bowie, 2004; Schultz et al., 1997). The structures of a number of isolated SAM domains and of SAM domains in complexes have been solved (Smalla et al., 1999; Stapleton et al., 1999; Thanos et al., 1999a; Thanos et al., 1999b), revealing a relatively well conserved fold consisting of 5 alpha-helices, although some deviations in helix angles, if not limits -and in one case also in the number of helices-have been noted (Kwan and Donaldson, 2007). Several, but far from all SAM domains are known to homodimerize and/or heterodimerize (Ramachander and Bowie, 2004), but the rules for the different behaviors are just emerging (Meruelo and Bowie, 2009). "
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    ABSTRACT: The sterile alpha motif (SAM) for protein-protein interactions is encountered in over 200 proteins, but the structural basis for its interactions is just becoming clear. Here we solved the structure of the EphA2-SHIP2 SAM:SAM heterodimeric complex by use of NMR restraints from chemical shift perturbations, NOE and RDC experiments. Specific contacts between the protein surfaces differ significantly from a previous model and other SAM:SAM complexes. Molecular dynamics and docking simulations indicate fluctuations in the complex toward alternate, higher energy conformations. The interface suggests that EphA family members bind to SHIP2 SAM, whereas EphB members may not; correspondingly, we demonstrate binding of EphA1, but not of EphB2, to SHIP2. A variant of EphB2 SAM was designed that binds SHIP2. Functional characterization of a mutant EphA2 compromised in SHIP2 binding reveals two previously unrecognized functions of SHIP2 in suppressing ligand-induced activation of EphA2 and in promoting receptor coordinated chemotactic cell migration.
    Full-text · Article · Jan 2012 · Structure
    • "The ∼70-amino acid SAM domains are found in over 200 human proteins and are known to serve as protein-protein interaction domains (14). However, the recent structural determinations of the DLC-2 SAM domain suggest that this SAM domain is structurally distinct and hence may be functionally distinct from canonical SAM domains (15, 16). The RhoGAP domain of DLC-1 has been shown to stimulate RhoA inactivation in vitro and in vivo (5, 17). "
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    ABSTRACT: DLC-1 encodes a Rho GTPase-activating protein (RhoGAP) and negative regulator of specific Rho family proteins (RhoA-C and Cdc42). DLC-1 is a multi-domain protein, with the RhoGAP catalytic domain flanked by an amino-terminal sterile alpha motif (SAM) and a carboxyl-terminal START domain. The roles of these domains in the regulation of DLC-1 function remain to be determined. We undertook a structure-function analysis involving truncation and missense mutants of DLC-1. We determined that the amino-terminal SAM domain functions as an autoinhibitory domain of intrinsic RhoGAP activity. Additionally, we determined that the SAM and START domains are dispensable for DLC-1 association with focal adhesions. We then characterized several mutants for their ability to regulate cell migration and identified constitutively activated and dominant negative mutants of DLC-1. We report that DLC-1 activation profoundly alters cell morphology, enhances protrusive activity, and can increase the velocity but reduce directionality of cell migration. Conversely, the expression of the amino-terminal domain of DLC-1 acts as a dominant negative and profoundly inhibits cell migration by displacing endogenous DLC-1 from focal adhesions.
    No preview · Article · Oct 2008 · Journal of Biological Chemistry
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