PDBsum entry 3cw3

Oncoprotein

PDB id: 3cw3

Contents

Protein chain

93 a.a.

Ligands

GOL

Waters ×110

References listed in PDB file

Key reference

Title

Exploring the limits of sequence and structure in a variant betagamma-Crystallin domain of the protein absent in melanoma-1 (aim1).

Authors

P.Aravind, G.Wistow, Y.Sharma, R.Sankaranarayanan.

Ref.

J Mol Biol, 2008, 381, 509-518. [DOI no: 10.1016/j.jmb.2008.06.019]

PubMed id

18582473

Abstract

Betagamma-crystallins belong to a superfamily of proteins in prokaryotes and eukaryotes that are based on duplications of a characteristic, highly conserved Greek key motif. Most members of the superfamily in vertebrates are structural proteins of the eye lens that contain four motifs arranged as two structural domains. Absent in melanoma 1 (AIM1), an unusual member of the superfamily whose expression is associated with suppression of malignancy in melanoma, contains 12 betagamma-crystallin motifs in six domains. Some of these motifs diverge considerably from the canonical motif sequence. AIM1g1, the first betagamma-crystallin domain of AIM1, is the most variant of betagamma-crystallin domains currently known. In order to understand the limits of sequence variation on the structure, we report the crystal structure of AIM1g1 at 1.9 A resolution. Despite having changes in key residues, the domain retains the overall betagamma-crystallin fold. The domain also contains an unusual extended surface loop that significantly alters the shape of the domain and its charge profile. This structure illustrates the resilience of the betagamma fold to considerable sequence changes and its remarkable ability to adapt for novel functions.

Figure 2.
Fig. 2. (a) 3-D structure of the AIM1g1 domain. The secondary structural elements have been marked. The third strand (β3) is marked despite its looplike appearance for greater clarity, as it deviates only partly from the strand architecture and is a conserved feature among all vertebrate βγ-crystallins. (b) Topology of AIM1g1 is depicted showing the presence of the twin Greek key motifs (A and B) with the large twisted loop 2 connecting β7 and β8. (c) Overlap of γB crystallin and βB2 crystallin N-terminal domains with AIM1g1. Grey indicates the backbone of AIM1g1, cyan represents γB crystallin and magenta represents βB2-crystallin domain. The first hairpin of AIM1g1 is splayed due to disorder. Loop 2 clearly shows completely different orientation as compared to the lens βγ-crystallin domains. Extent of overlap is in accordance with values given in Table 2 for structural relatedness that was analyzed by the DaliLite program of EBI.^17 The purified protein was crystallized using a 2 μl + 2 μl mixture of protein and a reservoir solution containing 1.3–1.4 M sodium citrate, 0.1 M Hepes, pH 7.3–7.5, with nonpolar solvents such as isopropanol (1–3%), DMSO (2%) and salts such as ammonium sulfate (0.06 M) and sodium chloride (0.4 M) as additives.^18 Different heavy-atom compounds such as thiomersal, cadmium chloride and sodium iodide were initially attempted by soaking crystals in high concentrations (10–50 mM) of these solutions and observing the crystals for morphological changes. Both time of soak and concentration of the soak were altered to get well-diffracting isomorphous derivatives. All derivatized crystals were transferred to 15% glycerol solution containing the heavy atom before being flash-frozen at 100 K. Data were collected over large sectors to collect the anomalous signal for the heavy atom especially for iodide derivative, as iodine is known to have high anomalous signal when CuKα X-rays are used.^19 Good derivatives and native data were then scaled together and phasing was performed using the program SOLVE. Solve picked up six sites, three each for iodine derivative and cadmium derivative, and yielded a mean figure of merit ( angle bracket m angle bracket ) of 0.51 up to a resolution of 2.1 Å with good electron density maps depicting clear β-strands in the map built without density modification. Density modification and automated model building was done by Resolve, which built up to vert, similar 80% of the main chain with vert, similar 60% of the side chains. Manual model building was performed using the program O.

Figure 3.
Fig. 3. (a) The Tyr corner, which is an important feature in other domains, is replaced to Leu63 in AIM1g1. There are no major effects on the fold of the molecule in spite of this mutation. (b) The Trp corner, one of the features conserved among AIM1g1 and lens crystallins, and its interactions in the hydrophobic core. It acts as a bridge between A and B motifs. (c) Surface representation of AIM1g1 showing strong electronegative charge distribution in the loop region of the domain. Surface representation was done using GRASP.^24 (d) Extensive water networking is observed in the loop region. Water molecules involved in formation of hydrogen-bond connectivities are w118, w121, w126, w128 w147, w151, w157, w161, w171, w190, w212 and w216 along with a glycerol molecule found in the vicinity of the loop. These water molecules bridge the side chains, main-chain atoms and help in stabilization. These interactions are in addition to the electrostatic interactions that hold crystal lattice intact.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 509-518) copyright 2008.