Domains dimers

This model of Cro binding to DNA was arrived at by intuition and clever model building. Its validity was considerably strengthened when the same features were subsequently found in the DNA-binding domains of the lambda-repressor molecule. The helix-turn-helix motif with a recognition helix is present in the repressor, and moreover the repressor DNA-binding domains dimerize in the crystals in such a way that the recognition helices are separated by 34 A as in Cro. 

Figure 3.7 The crystal structure of DtxR, a 226-residue three-domain dimeric protein, is shown. The protein, activated by cobalt (designated 1 and 2), is bound to a 21-bp DNA duplex based on the consensus operator sequence. Two DtxR dimers surround the DNA duplex, which is distorted compared to canonical B-DNA. Only domain 1, involved in DNA-binding, and domain 2, involved in dimer formation, are shown. The helices of the DNA-binding domain are indicated by HI, H2, and H3. H3 binds to the major groove of the DNA. From Pohl et al., 1999, by permission of Academic Press. 

Fig. 3. Structures of prion protein globular domains. (A) Crystal structure of the C-terminal domain dimer of Ure2p (pdb file 1HQO). (B) NMR structure of the C-terminal domain monomer of PrP (pdb file 1E1G).

Fig. 2. Molecular model of the eNOS heme domain dimer. Each monomer consists of residues 69-482. The pterin is depicted as a space-filled model and the hemes are the white stick models. The single Zn ion situated at the lower part of the dimer interface is depicted as the white ball. The overall fold is unique to NOS.

Fig. 9.10. Ligation of two protein fragments by trans-splicing interns a) on the DNA level, the two fragments can be encoded in separate ORFs and are flanked by either a 3 -extension encoding the N-intein (N-fragment) or 5 -extension encoding the C-intein (C-fragment). b) Following transcription and translation, the intein domains dimerize and c) excise themselves, fusing the N- and C-fragment by a peptide backbone bond.

Ho WC, Fitzgerald MX, Marmorstein R (2006) Structure of the p53 core domain dimer bound to DNA. J Biol Chem 281 20494-20502... 

Figure 3 Steady-state shapes upon binding of the Amphiphysin N-BAR domain dimer plots show upper leaflet contours of membranes with different bending rigidities and with N-helix insertions of various depths. The membrane patches have -0.4e/nm2 average surface charge densities (corresponding to 0.3 PS lipid fractions) on both layers. The orientation of the BAR domain used in these calculations is the same as in Figure 2. For all systems, a nonzero spontaneous curvature c0 domain was defined for a membrane patch inside the BAR projection area shown in panel L and extending 20 A away from the projected zone. The values for c0 in the range of 0-1/70 A 1 were used.

The STAT proteins have an N-terminal oligomerization domain, an SH3 and an SH3 domain, a DNA binding domain and a C-terminal transactivation domain. Dimerization is mediated by the phosphotyrosine residue and the SH2 domain. Highly resolved structural investigation show that the phosphotyrosine residue of one Stat protein binds to the SH2 domain of the partner and vice versa, so that the phospho-tyrosine-SH2 bonds function as a double clasp (structure in complex with DNA Becker et al., 1998). The binding to DNA is in the form of a dimer, with the Stat-DNA... 

Feltham R, Bettjeman B, Budhidarmo R et al (2011) Smac mimetics activate the E3 ligase activity of cIAPl protein by promoting RING domain dimerization. J Biol Chem 286(19) 17015-17028... 

Figure 13 Structure of the N-terminal domain dimer of riboflavin synthase from Escherichia coli (PDB entry 1PKV) with bound riboflavin viewed along the twofold noncrystallographic symmetry axis.

Economides et al. conjugated three protein chains, one heavy chain from an antibody Fc domain, interleukin-6 (ILfiRa), and gpl30. The Fc domain dimerizes to yield a tetravalent molecule with two ILfiRo and two gpl30 receptors. These authors report that this protein fusion system potently blocks cytokines in vitro and in vivo, representing a substantial advance in creating novel therapeutic candidates for cytokine-driven diseases. 

Substrate Specificity of Ketosynthase Domains. .. Dimeric Monomeric... 

The 54 kDa wc-2 protein (WC-2) contains a nuclear-targeting domain and a PAS domain. Both the mRNA and protein are constitutively expressed, and the polypeptide appears to undergo no circadian phase-dependent modifications, though it is phosphorylated in response to light.The WC-2 PAS domain dimerizes with itself and with WC-1 via its PAS domain, forming hetero- and homodimers in vitro and in vivo. > Together, WC-1 and WC-2 form the white collar complex (WCC) in which both proteins appear in a 1 1 stoichiometry. This differs from the cellular concentrations of the two... 

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