| SMART accession number: | SM00201
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| Description: |
Somatomedin-B is a peptide, proteolytically excised from vitronectin, that is a growth hormone-dependent serum factor with protease-inhibiting activity. |
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| Interpro abstract (IPR001212): |
Somatomedin B (SMB), a serum factor of unknown function, is a small cysteine-rich peptide, derived proteolytically from the N terminus of the cell-substrate adhesion protein vitronectin [(PUBMED:2447940)]. Cys-rich somatomedin B-like domains are found in a number of proteins [(PUBMED:1710108)], including plasma-cell membrane glycoprotein (which has nucleotide pyrophosphate and alkaline phosphodiesterase I activities) [(PUBMED:1647027)] and placental protein 11, which appears to possess amidolytic activity. 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 homodimerisation [(PUBMED:12533192)]. The SMB domain contains eight Cys residues, arranged into four disulphide bonds. It has been suggested that the active SMB domain may be permitted considerable disulphide bond heterogeneity or variability, provided that the Cys25-Cys31 disulphide bond is preserved. The three dimensional structure of the SMB domain is extremely compact and the disulphide bonds are packed in the centre of the domain forming a covalently bonded core [(PUBMED:15157085)]. The structure of the SMB domain presents a new protein fold, with the only ordered secondary structure being a single-turn alpha-helix and a single-turn 3(10)-helix [(PUBMED:12808446)].
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| GO process: | immune response (GO:0006955) |
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| GO function: | scavenger receptor activity (GO:0005044), polysaccharide binding (GO:0030247) |
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| Family alignment: |
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Click on the following links for more information.
- Evolution (species in which this domain is found)
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- Literature (relevant references for this domain)
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Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Jenne D
- Homology of placental protein 11 and pea seed albumin 2 with vitronectin.
- Biochem Biophys Res Commun. 1991; 176: 1000-6
- Display abstract
Vitronectin (complement S-protein), a plasma and tissue glycoprotein of 75 kDa, shares the amino-terminal somatomedin B domain with the membrane glycoprotein PC1 of plasma cells and several hemopexin-type repeats with hemopexin and the non-catalytic carboxy-terminal domain of collagenases. It serves as a ligand for certain integrin receptors, binds to distinct members of the serpin family and inhibits the pore-forming cytolytic reaction of the terminal complement pathway. Computer-assisted data base searches revealed the presence of a single somatomedin B domain in the recently cloned placental protein 11, and four hemopexin-type repeats in the cytosolic plant protein PA2, the major albumin of pea seeds, whose function is unknown. Our finding shows that hemopexin-type repeats are present in extracellular as well as in cytosolic proteins and most likely originated before the divergence of the animal and plant kindoms.
- Seiffert D, Loskutoff DJ
- Evidence that type 1 plasminogen activator inhibitor binds to the somatomedin B domain of vitronectin.
- J Biol Chem. 1991; 266: 2824-30
- Display abstract
The interaction between type 1 plasminogen activator inhibitor (PAI-1) and fragments of vitronectin (Vn) was investigated. The PAI-1-binding domain was not destroyed when Vn was cleaved by treatment with either acid or CNBr. Acid-cleaved Vn was fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and analyzed by PAI-1 ligand binding. The smallest fragment (Mr 40,000) that retained PAI-1 binding function was sequenced and shown to contain the NH2 terminus of the molecule. Further cleavage of this fragment by treatment with CNBr generated a Mr 35,000 fragment (Pro52-Asp239) that did not interact with PAI-1, and a Mr 6,000 NH2-terminal fragment (Asp1-Met51) that spanned the somatomedin B domain and contained the RGD (cell binding) sequence. The purified Mr 6,000 fragment competed with immobilized Vn for PAI-1 binding, and formed complexes with activated PAI-1. These complexes could be immunoprecipitated by antibodies to PAI-1. Synthetic peptides containing the RGD sequence had no effect on the binding of this fragment to PAI-1. These results suggest that the cell-binding and PAI-1 binding sequences of Vn occupy distinct regions in the NH2-terminal somatomedin B domain of the molecule.
- Patthy L
- Detecting distant homologies of mosaic proteins. Analysis of the sequences of thrombomodulin, thrombospondin complement components C9, C8 alpha and C8 beta, vitronectin and plasma cell membrane glycoprotein PC-1.
- J Mol Biol. 1988; 202: 689-96
- Display abstract
Recognition of homologies may give hints about the structure and function of proteins; therefore, we are developing strategies to aid sequence comparisons. Detecting homology of mosaic proteins is especially difficult since the modules constituting these proteins are usually distantly related and their homology is not readily recognized by conventional computer programs. In the present work we show that the rules of the evolution of mosaic proteins can guide the identification of modules of mosaic proteins and can delineate the group of sequences in which the presence of homologous sequences may be expected. By this approach we can concentrate the search for homology to a limited group of sequences; thus ensuring a more intense and more fruitful search. The power of this approach is illustrated by the fact that it could detect homologies not identified by earlier methods of sequence comparison. In this paper we show that thrombomodulin contains a domain homologous with animal lectins, that complement components C9, C8 alpha and C8 beta have modules homologous with one of the repeat units of thrombospondin and that the somatomedin B module of vitronectin is homologous with the internal repeats of plasma cell membrane glycoprotein PC-1.
- Disease (disease genes where sequence variants are found in this domain)
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SwissProt sequences and OMIM curated human diseases associated with missense mutations within the SO domain.
- Metabolism (metabolic pathways involving proteins which contain this domain)
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Click the image to view the interactive version of the map in iPath | | % proteins involved | KEGG pathway ID | Description |
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| 36.36 |  map00565 | Ether lipid metabolism | | 31.82 | map04512 | ECM-receptor interaction | | 31.82 | map04510 | Focal adhesion |
This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with SO domain which could be assigned to a KEGG orthologous group, and not all proteins containing SO domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%. |
- Structure (3D structures containing this domain)
3D Structures of SO domains in PDB
| PDB code | Main view | Title | | 1oc0 |  | Plasminogen activator inhibitor-1 complex with somatomedin b domain of vitronectin |
| 1s4g |  | Somatomedin-b domain of human plasma vitronectin. |
| 1ssu |  | Structural and biochemical evidence for disulfide bond heterogeneity in active forms of the somatomedin b domain of human vitronectin |
| 2cqw |  | Solution structure of rsgi ruh-041, a smb-like domain from mouse cdna |
| 2jq8 |  | Solution structure of the somatomedin b domain from vitronectin produced in pichia pastoris |
| 2ys0 |  | Solution structure of the somatomedin b domain of human ectonucleotide pyrophosphatase/phosphodiesterase family member |
| 3bt1 |  | Structure of urokinase receptor, urokinase and vitronectin complex |
| 3bt2 |  | Structure of urokinase receptor, urokinase and vitronectin complex |
- Links (links to other resources describing this domain)
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to expand nodes. To display all proteins with a SO domain in a specific node, click on it.