SBDS

Ribosome maturation protein SBDS is a protein that in humans is encoded by the SBDS gene. An alternative transcript has been described, but its biological nature has not been determined. This gene has a closely linked pseudogene that is distally located. This gene encodes a member of a highly conserved protein family that exists in all archaea and eukaryotes.

Function

The encoded protein plays an essential role in ribosome biogenesis. SBDS interacts with elongation factor-like GTPase 1 (Efl1) to disassociate eukaryotic initiation factor 6 (eIF6) from the late cytoplasmic pre-60S ribosomal subunit allowing assembly of the 80S. Dynamic rotation of the SBDS protein in the ribosomal P site is coupled to a conformational switch in EFL1 that promotes eIF6 displacement through competition for an overlapping binding site on the 60S ribosomal subunit. Yeast SBDS ortholog, Sdo1, functions within a pathway containing Efl1 to facilitate the release and recycling of the nucleolar shuttling factor Tif6 (yeast eIF6 ortholog) from late cytoplasmic pre-60S ribosomal subunit. Knockdown of SBDS expression results in increased apoptosis in erythroid cells undergoing differentiation due to elevated ROSTooltip reactive oxygen species levels. Hence SBDS is critical for normal erythropoiesis.

This family is highly conserved in species ranging from archaea to vertebrates and plants. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. Members of this family play a role in RNA metabolism.

A number of uncharacterised hydrophilic proteins of about 30 kDa share regions of similarity. These include,

• Mouse protein 22A3.
• Saccharomyces cerevisiae chromosome XII hypothetical protein YLR022c.
• Caenorhabditis elegans hypothetical protein W06E11.4.
• Methanococcus jannaschii hypothetical protein MJ0592.

This particular protein sequence is highly conserved in species ranging from archaea to vertebrates and plants.

Structure

The SBDS protein contains three domains, an N-terminal conserved FYSH domain, central helical domain and C-terminal domain containing an RNA-binding motif.

N-terminal domain

SBDS protein N-terminal domain
Identifiers
Symbol	SBDS
Pfam	PF01172
InterPro	IPR019783
PROSITE	PDOC00974
SCOP2	1nyn / SCOPe / SUPFAM
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

This protein domain appears to be very important, since mutations in this domain are usually the cause of Shwachman-Bodian-Diamond syndrome. It shares distant structural and sequence homology to a protein named YHR087W found in the yeast Saccharomyces cerevisiae. The protein YHR087W is involved in RNA metabolism, so it is probable that the SBDS N-terminal domain has the same function.

The N-terminal domains contains a novel mixed alphabeta fold, four beta-strands, and four alpha-helices arranged as a three beta stranded anti-parallel-sheet.

Central domain

The function of this protein domain has been difficult to elucidate. It is possible that it has a role in binding to DNA or RNA. Protein binding to form a protein complex is also another possibility. It has been difficult to infer the function from the structure since this particular domain structure is found in archea.

This domain contains a very common structure, the winged helix-turn-helix.

C-terminal domain

SBDS protein C-terminal domain
Identifiers
Symbol	SBDS_C
Pfam	PF09377
InterPro	IPR018978
SCOP2	1nyn / SCOPe / SUPFAM
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

In molecular biology, the SBDS C-terminal protein domain is highly conserved in species ranging from archaea to vertebrates and plants.

Members of this family are thought to play a role in RNA metabolism. However, its precise function remains to be elucidated. Furthermore, its structure makes it very difficult to predict the protein domain's function.

The structure of the C-terminal domain contains a ferredoxin-like fold This structure has a four-stranded beta-sheet with two helices on one side.

Clinical significance

Mutations within this gene are associated with Shwachman-Bodian-Diamond syndrome. The two most common mutations associated with this syndrome are at positions 183–184 (TA→CT) resulting in a premature stop-codon (K62X) and a frameshift mutation at position 258 (2T→C) resulting in a stopcodon (C84fsX3).

External links

• GeneReviews/NIH/NCBI/UW entry on Shwachman-Diamond Syndrome
• Overview of all the structural information available in the PDB for UniProt: Q9Y3A5 (Ribosome maturation protein SBDS) at the PDBe-KB.

This article incorporates text from the public domain Pfam and InterPro: IPR002140