Limits...
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

Structure and topology of hDSPRY. (a) Topology map with β-sheet 1 coloured blue, β-sheet 2 red and β-sheet 3 green. β-Strands are illustrated as arrows. The artificial β-addition module, β-strand 16, of chain B is shown in grey. (b) The β-sandwich fold of hDSPRY; colouring is similar to that in (a). Loop D is highlighted in purple.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4555926&req=5

fig2: Structure and topology of hDSPRY. (a) Topology map with β-sheet 1 coloured blue, β-sheet 2 red and β-sheet 3 green. β-Strands are illustrated as arrows. The artificial β-addition module, β-strand 16, of chain B is shown in grey. (b) The β-sandwich fold of hDSPRY; colouring is similar to that in (a). Loop D is highlighted in purple.

Mentions: hDSPRY adopts a compact β-sandwich conformation. All secondary-structure elements form β-strands (Fig. 2 ▸a) and in contrast to other SPRY domains (Chen et al., 2012 ▸; Park et al., 2010 ▸; D’Cruz, Kershaw et al., 2013 ▸; Weinert et al., 2009 ▸) no α-helical regions could be found in the N- and C-termini. The β-sandwich fold is slightly twisted and forms a bowl-like platform. Two layers of concave β-sheets stack together and are referred to in the following as β-sheets 1 and 2, and a third small β-sheet covers one side of the β-sandwich (Fig. 2 ▸). β-Sheet 1 is composed of eight strands (β16, β1, β4, β13, β7, β8, β9 and β10), β-sheet 2 is composed of six strands (β2, β3, β14, β6, β11 and β12) and the small β-sheet 3 consists of only two strands (β15 and β5). All β-strands of the β-sandwich core are arranged in an antiparallel configuration, except for strands β16 and β1, which are oriented parallel. Interestingly, strand β16 is only observed in the model of chain B as it consists of the four additional residues that could be modelled at the C-terminus (residues 276–279) of chain A. It is held in place by hydrogen bonds to strand β1 and forms a β-addition module, which might be an artifact of crystal packing. On one hand, the residues of strand β16 in the model of chain B do not belong to the SPRY core domain (Fig. 2 ▸a and Supplementary Fig. S4). On the other hand, the C-terminal loop region in the model of chain A adopts a totally different conformation to that in chain B and points away from the SPRY domain.


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)

Structure and topology of hDSPRY. (a) Topology map with β-sheet 1 coloured blue, β-sheet 2 red and β-sheet 3 green. β-Strands are illustrated as arrows. The artificial β-addition module, β-strand 16, of chain B is shown in grey. (b) The β-sandwich fold of hDSPRY; colouring is similar to that in (a). Loop D is highlighted in purple.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4555926&req=5

fig2: Structure and topology of hDSPRY. (a) Topology map with β-sheet 1 coloured blue, β-sheet 2 red and β-sheet 3 green. β-Strands are illustrated as arrows. The artificial β-addition module, β-strand 16, of chain B is shown in grey. (b) The β-sandwich fold of hDSPRY; colouring is similar to that in (a). Loop D is highlighted in purple.
Mentions: hDSPRY adopts a compact β-sandwich conformation. All secondary-structure elements form β-strands (Fig. 2 ▸a) and in contrast to other SPRY domains (Chen et al., 2012 ▸; Park et al., 2010 ▸; D’Cruz, Kershaw et al., 2013 ▸; Weinert et al., 2009 ▸) no α-helical regions could be found in the N- and C-termini. The β-sandwich fold is slightly twisted and forms a bowl-like platform. Two layers of concave β-sheets stack together and are referred to in the following as β-sheets 1 and 2, and a third small β-sheet covers one side of the β-sandwich (Fig. 2 ▸). β-Sheet 1 is composed of eight strands (β16, β1, β4, β13, β7, β8, β9 and β10), β-sheet 2 is composed of six strands (β2, β3, β14, β6, β11 and β12) and the small β-sheet 3 consists of only two strands (β15 and β5). All β-strands of the β-sandwich core are arranged in an antiparallel configuration, except for strands β16 and β1, which are oriented parallel. Interestingly, strand β16 is only observed in the model of chain B as it consists of the four additional residues that could be modelled at the C-terminus (residues 276–279) of chain A. It is held in place by hydrogen bonds to strand β1 and forms a β-addition module, which might be an artifact of crystal packing. On one hand, the residues of strand β16 in the model of chain B do not belong to the SPRY core domain (Fig. 2 ▸a and Supplementary Fig. S4). On the other hand, the C-terminal loop region in the model of chain A adopts a totally different conformation to that in chain B and points away from the SPRY domain.

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