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PROSITE documentation PDOC00453 [for PROSITE entry PS00524]

Somatomedin B (SMB) domain signature and profile





Description

Somatomedin B, a serum factor of unknown function, is a cysteine-rich 44 residues peptide which is proteolytically derived from the N-terminal extremity of the cell-substrate adhesion protein vitronectin [1]. Somatomedin B-like (SMB) domains are also found [2,3] in the following proteins:

  • Ubiquitous nucleotide pyrophosphatase/phosphodiesterases NPP1-3. NPP1-3 release 5'monophosphorylated nucleotides from a variety of nucleotides and nucleotide derivatives. In addition, NPP1-3 contain intrinsic alkaline phosphatase activity. They consist of a short cytoplasmic N-terminal domain, a single transmembrane domain and a large extracellular part, comprising two somatomedin-B-like domains, a catalytic domain and a poorly defined C-terminal domain.
  • Placental protein 11 (PP11) (EC 3.4.21.-). PP11 is a placental protein that seems to possess an amidolytic activity. A copy of the somatomedin B domain is present at the N-terminal extremity.
  • Secreted proteoglycan known as superficial zone protein.
  • Some amphibian DNases.
  • Drosophila macrophage-specific Scavenger receptor.

The SMB domain of vitronectin has been demonstrated to interact with both the urokinase receptor and the plasminogen activator inhibitor-1 (PAI-1) and the conserved cysteines of the NPP1 somatomedin B-like domain have been shown to mediate homodimerization [3].

As shown in the following schematic representation below the SMB domain contains eight Cys residues, arranged into four disulfide bonds. It has been suggested that the active SMB domain may be permitted considerable disulfide bond heterogeneity or variability, provided that the Cys25-Cys31 disulfide bond is preserved. The three dimensional structure of the SMB domain is extremely compact and the disulfide bonds are packed in the center of the domain forming a covalently bonded core [4]. The structure of the SMB domain presents a new protein fold, with the only ordered secondary structure being a single-turn α-helix and a single-turn 3(10)-helix (see <PDB:1OC0>) [5].

         xxCxxxxxxCxxxxxxxxxCxCxxxCxxxxxCCxxxxxCxxxxx
                            ********************
'C': conserved cysteine probably involved in a disulfide bond.
'*': position of the pattern.

The profile we developed covers the entire SMB domain.

Expert(s) to contact by email:

Jenne D.

Last update:

December 2004 / Pattern and text revised.

Technical section

PROSITE methods (with tools and information) covered by this documentation:

SMB_1, PS00524; Somatomedin B domain (SMB) signature  (PATTERN)

SMB_2, PS50958; Somatomedin B (SMB) domain profile  (MATRIX)


References

1AuthorsJenne D. Stanley K.K.
TitleNucleotide sequence and organization of the human S-protein gene: repeating peptide motifs in the 'pexin' family and a model for their evolution.
SourceBiochemistry 26:6735-6742(1987).
PubMed ID2447940

2AuthorsJenne D.
TitleHomology of placental protein 11 and pea seed albumin 2 with vitronectin.
SourceBiochem. Biophys. Res. Commun. 176:1000-1006(1991).
PubMed ID1710108

3AuthorsGijsbers R. Ceulemans H. Bollen M.
TitleFunctional characterization of the non-catalytic ectodomains of the nucleotide pyrophosphatase/phosphodiesterase NPP1.
SourceBiochem. J. 371:321-330(2003).
PubMed ID12533192
DOI10.1042/BJ20021943

4AuthorsKamikubo Y. De Guzman R. Kroon G. Curriden S. Neels J.G. Churchill M.J. Dawson P. Oldziej S. Jagielska A. Scheraga H.A. Loskutoff D.J. Dyson H.J.
TitleDisulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin.
SourceBiochemistry 43:6519-6534(2004).
PubMed ID15157085
DOI10.1021/bi049647c

5AuthorsZhou A. Huntington J.A. Pannu N.S. Carrell R.W. Read R.J.
TitleHow vitronectin binds PAI-1 to modulate fibrinolysis and cell migration.
SourceNat. Struct. Biol. 10:541-544(2003).
PubMed ID12808446
DOI10.1038/nsb943



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