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Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein.

Kellner JN, Meinhart A - Acta Crystallogr F Struct Biol Commun (2015)

Bottom Line: Interestingly, though, a conserved patch of positive surface charge is found that may replace the connecting loops as a protein-protein interaction surface.The data presented here comprise the first structural information on DDX1 and provide insights into the unique domain architecture of this DEAD-box protein.By providing the structure of a putative interaction domain of DDX1, this work will serve as a basis for further studies of the interaction network within the hetero-oligomeric complexes of DDX1 and of its recruitment to the HIV-1 Rev protein as a viral replication factor.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.

ABSTRACT
The human RNA helicase DDX1 in the DEAD-box family plays an important role in RNA processing and has been associated with HIV-1 replication and tumour progression. Whereas previously described DEAD-box proteins have a structurally conserved core, DDX1 shows a unique structural feature: a large SPRY-domain insertion in its RecA-like consensus fold. SPRY domains are known to function as protein-protein interaction platforms. Here, the crystal structure of the SPRY domain of human DDX1 (hDSPRY) is reported at 2.0 Å resolution. The structure reveals two layers of concave, antiparallel β-sheets that stack onto each other and a third β-sheet beneath the β-sandwich. A comparison with SPRY-domain structures from other eukaryotic proteins showed that the general β-sandwich fold is conserved; however, differences were detected in the loop regions, which were identified in other SPRY domains to be essential for interaction with cognate partners. In contrast, in hDSPRY these loop regions are not strictly conserved across species. Interestingly, though, a conserved patch of positive surface charge is found that may replace the connecting loops as a protein-protein interaction surface. The data presented here comprise the first structural information on DDX1 and provide insights into the unique domain architecture of this DEAD-box protein. By providing the structure of a putative interaction domain of DDX1, this work will serve as a basis for further studies of the interaction network within the hetero-oligomeric complexes of DDX1 and of its recruitment to the HIV-1 Rev protein as a viral replication factor.

No MeSH data available.


Related in: MedlinePlus

Sequence conservation of the SPRY domain amongst DDX1 homologues. (a) Sequence alignment of hDSPRY with the SPRY domains of DDX1 homologues from eukaryotic model organisms. Conservation values were determined using the AMAS server (Livingstone & Barton, 1993 ▸) and are indicated by colour coding (dark green for identical residues to yellow for less homologous residues). Residues of the hydrophobic core that stabilize the domain fold are indicated by diamonds, residues of surface A are indicated by grey circles and residues of the conserved, positively charged surface patch of hDSPRY are indicated by triangles. Secondary-structure elements are shown above the sequence alignment and are coloured according to Fig. 1 ▸. Residues that could be modelled in the crystal structure (residues 86–279) are indicated in grey and domain boundaries of the crystallization construct are indicated in brown (residues 72–283). (b) Sequence conservation mapped onto the molecular surface of hDSPRY. (c) Electrostatic surface potential, calculated using APBS (Baker et al., 2001 ▸), mapped onto the molecular surface.
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fig5: Sequence conservation of the SPRY domain amongst DDX1 homologues. (a) Sequence alignment of hDSPRY with the SPRY domains of DDX1 homologues from eukaryotic model organisms. Conservation values were determined using the AMAS server (Livingstone & Barton, 1993 ▸) and are indicated by colour coding (dark green for identical residues to yellow for less homologous residues). Residues of the hydrophobic core that stabilize the domain fold are indicated by diamonds, residues of surface A are indicated by grey circles and residues of the conserved, positively charged surface patch of hDSPRY are indicated by triangles. Secondary-structure elements are shown above the sequence alignment and are coloured according to Fig. 1 ▸. Residues that could be modelled in the crystal structure (residues 86–279) are indicated in grey and domain boundaries of the crystallization construct are indicated in brown (residues 72–283). (b) Sequence conservation mapped onto the molecular surface of hDSPRY. (c) Electrostatic surface potential, calculated using APBS (Baker et al., 2001 ▸), mapped onto the molecular surface.

Mentions: DDX1 is widespread in eukaryotic organisms and, in addition to the RecA-like domains (Supplementary Fig. S4), the SPRY domain is also highly conserved (Fig. 5 ▸a). The residues of the hydrophobic core stabilizing the β-sandwich fold in hDSPRY were found to be either conserved or substituted with similar hydrophobic residues (Fig. 5 ▸a). The residues of most β-strands are conserved, except for those of two β-strands at the C-terminus: β-strand β15 of β-sheet 3 and the potentially artificial strand β16. Interestingly, the degree of conservation varies between the two sheets, and residues that are part of β-sheet 1 are virtually identical in DDX1 orthologues, whereas the residues of β-sheet 2, mostly of strands β2, β12 and β14, are less conserved (Fig. 5 ▸a). Nevertheless, the residues of the hydrophobic core are still conserved. Notably, the N- and C-terminal regions of the SPRY domain are not conserved at all and belong to the few loop regions that significantly differ in amino-acid sequence and length (4–9 residues) in DDX1 (Supplementary Fig. S4). The residues at these termini correspond to the regions that connect the compact SPRY domain to the RecA-like domain 1 of the DDX1 protein core. Conservation of these linker regions is most likely to be dispensable for DDX1 function, and thus these regions lack any evolutionary selective pressure for sequence maintenance. In addition to these linker regions, most of the loop regions in hDSPRY are also not well conserved and differences in the number of residues are also found in some of the loop regions (Fig. 5 ▸a).


Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein.

Kellner JN, Meinhart A - Acta Crystallogr F Struct Biol Commun (2015)

Sequence conservation of the SPRY domain amongst DDX1 homologues. (a) Sequence alignment of hDSPRY with the SPRY domains of DDX1 homologues from eukaryotic model organisms. Conservation values were determined using the AMAS server (Livingstone & Barton, 1993 ▸) and are indicated by colour coding (dark green for identical residues to yellow for less homologous residues). Residues of the hydrophobic core that stabilize the domain fold are indicated by diamonds, residues of surface A are indicated by grey circles and residues of the conserved, positively charged surface patch of hDSPRY are indicated by triangles. Secondary-structure elements are shown above the sequence alignment and are coloured according to Fig. 1 ▸. Residues that could be modelled in the crystal structure (residues 86–279) are indicated in grey and domain boundaries of the crystallization construct are indicated in brown (residues 72–283). (b) Sequence conservation mapped onto the molecular surface of hDSPRY. (c) Electrostatic surface potential, calculated using APBS (Baker et al., 2001 ▸), mapped onto the molecular surface.
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fig5: Sequence conservation of the SPRY domain amongst DDX1 homologues. (a) Sequence alignment of hDSPRY with the SPRY domains of DDX1 homologues from eukaryotic model organisms. Conservation values were determined using the AMAS server (Livingstone & Barton, 1993 ▸) and are indicated by colour coding (dark green for identical residues to yellow for less homologous residues). Residues of the hydrophobic core that stabilize the domain fold are indicated by diamonds, residues of surface A are indicated by grey circles and residues of the conserved, positively charged surface patch of hDSPRY are indicated by triangles. Secondary-structure elements are shown above the sequence alignment and are coloured according to Fig. 1 ▸. Residues that could be modelled in the crystal structure (residues 86–279) are indicated in grey and domain boundaries of the crystallization construct are indicated in brown (residues 72–283). (b) Sequence conservation mapped onto the molecular surface of hDSPRY. (c) Electrostatic surface potential, calculated using APBS (Baker et al., 2001 ▸), mapped onto the molecular surface.
Mentions: DDX1 is widespread in eukaryotic organisms and, in addition to the RecA-like domains (Supplementary Fig. S4), the SPRY domain is also highly conserved (Fig. 5 ▸a). The residues of the hydrophobic core stabilizing the β-sandwich fold in hDSPRY were found to be either conserved or substituted with similar hydrophobic residues (Fig. 5 ▸a). The residues of most β-strands are conserved, except for those of two β-strands at the C-terminus: β-strand β15 of β-sheet 3 and the potentially artificial strand β16. Interestingly, the degree of conservation varies between the two sheets, and residues that are part of β-sheet 1 are virtually identical in DDX1 orthologues, whereas the residues of β-sheet 2, mostly of strands β2, β12 and β14, are less conserved (Fig. 5 ▸a). Nevertheless, the residues of the hydrophobic core are still conserved. Notably, the N- and C-terminal regions of the SPRY domain are not conserved at all and belong to the few loop regions that significantly differ in amino-acid sequence and length (4–9 residues) in DDX1 (Supplementary Fig. S4). The residues at these termini correspond to the regions that connect the compact SPRY domain to the RecA-like domain 1 of the DDX1 protein core. Conservation of these linker regions is most likely to be dispensable for DDX1 function, and thus these regions lack any evolutionary selective pressure for sequence maintenance. In addition to these linker regions, most of the loop regions in hDSPRY are also not well conserved and differences in the number of residues are also found in some of the loop regions (Fig. 5 ▸a).

Bottom Line: Interestingly, though, a conserved patch of positive surface charge is found that may replace the connecting loops as a protein-protein interaction surface.The data presented here comprise the first structural information on DDX1 and provide insights into the unique domain architecture of this DEAD-box protein.By providing the structure of a putative interaction domain of DDX1, this work will serve as a basis for further studies of the interaction network within the hetero-oligomeric complexes of DDX1 and of its recruitment to the HIV-1 Rev protein as a viral replication factor.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.

ABSTRACT
The human RNA helicase DDX1 in the DEAD-box family plays an important role in RNA processing and has been associated with HIV-1 replication and tumour progression. Whereas previously described DEAD-box proteins have a structurally conserved core, DDX1 shows a unique structural feature: a large SPRY-domain insertion in its RecA-like consensus fold. SPRY domains are known to function as protein-protein interaction platforms. Here, the crystal structure of the SPRY domain of human DDX1 (hDSPRY) is reported at 2.0 Å resolution. The structure reveals two layers of concave, antiparallel β-sheets that stack onto each other and a third β-sheet beneath the β-sandwich. A comparison with SPRY-domain structures from other eukaryotic proteins showed that the general β-sandwich fold is conserved; however, differences were detected in the loop regions, which were identified in other SPRY domains to be essential for interaction with cognate partners. In contrast, in hDSPRY these loop regions are not strictly conserved across species. Interestingly, though, a conserved patch of positive surface charge is found that may replace the connecting loops as a protein-protein interaction surface. The data presented here comprise the first structural information on DDX1 and provide insights into the unique domain architecture of this DEAD-box protein. By providing the structure of a putative interaction domain of DDX1, this work will serve as a basis for further studies of the interaction network within the hetero-oligomeric complexes of DDX1 and of its recruitment to the HIV-1 Rev protein as a viral replication factor.

No MeSH data available.


Related in: MedlinePlus