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| PROSITE documentation PDOC00453 |
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_2, PS50958; Somatomedin B (SMB) domain profile (MATRIX) |
| Sequences known to belong to this class detected by the profile: |
ALL |
| Other sequence(s) detected in Swiss-Prot: |
NONE. |
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| Matching PDB structures:
1OC0 1S4G 1SSU 2CQW ... [ALL] |
| SMB_1, PS00524; Somatomedin B domain (SMB) signature (PATTERN) |
| Consensus pattern: |
C-x-C-x(3)-C-x(5,6)-C-C-x-[DN]-[FY]-x(3)-C
|
| Sequences known to belong to this class detected by the pattern: |
ALL |
| Other sequence(s) detected in Swiss-Prot: |
NONE. |
|
|
|
| Matching PDB structures:
1OC0 1S4G 1SSU 2CQW ... [ALL] |
References:
| 1 |
Authors | Jenne D., Stanley K.K. |
| Title | Nucleotide sequence and organization of the human S-protein gene: repeating peptide motifs in the 'pexin' family and a model for their evolution. |
| Source | Biochemistry 26:6735-6742(1987). |
| PubMed ID | 2447940 |
| 2 |
Authors | Jenne D. |
| Title | Homology of placental protein 11 and pea seed albumin 2 with vitronectin. |
| Source | Biochem. Biophys. Res. Commun. 176:1000-1006(1991). |
| PubMed ID | 1710108 |
| 3 |
Authors | Gijsbers R., Ceulemans H., Bollen M. |
| Title | Functional characterization of the non-catalytic ectodomains of the nucleotide pyrophosphatase/phosphodiesterase NPP1. |
| Source | Biochem. J. 371:321-330(2003). |
| PubMed ID | 12533192 |
| DOI | 10.1042/BJ20021943 |
| 4 |
Authors | Kamikubo 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. |
| Title | Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin. |
| Source | Biochemistry 43:6519-6534(2004). |
| PubMed ID | 15157085 |
| DOI | 10.1021/bi049647c |
| 5 |
Authors | Zhou A., Huntington J.A., Pannu N.S., Carrell R.W., Read R.J. |
| Title | How vitronectin binds PAI-1 to modulate fibrinolysis and cell migration. |
| Source | Nat. Struct. Biol. 10:541-544(2003). |
| PubMed ID | 12808446 |
| DOI | 10.1038/nsb943 |
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