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24  structures 110  species 1  interaction 1147  sequences 76  architectures

Family: Somatomedin_B (PF01033)

Summary: Somatomedin B domain

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This is the Wikipedia entry entitled "Somatomedin B". More...

Somatomedin B Edit Wikipedia article

Somatomedin B domain
Identifiers
Symbol Somatomedin_B
Pfam PF01033
InterPro IPR001212
SMART SO
PROSITE PDOC00453

Somatomedin B is 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.[1] Cys-rich somatomedin B-like domains are found in a number of proteins,[2] including plasma-cell membrane glycoprotein (which has nucleotide pyrophosphate and alkaline phosphodiesterase I activities)[3] 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 homodimerization.[4] 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 centre of the domain forming a covalently bonded core.[5] 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.[6]

        xxCxxxxxxCxxxxxxxxxCxCxxxCxxxxxCCxxxxxCxxxxx
                           ********************

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

Human proteins containing this domain

ENPP1; ENPP2; ENPP3; PRG4; SUSD2; VTN;

References

  1. ^ Jenne D, Stanley KK (1987). "Nucleotide sequence and organization of the human S-protein gene: repeating peptide motifs in the "pexin" family and a model for their evolution". Biochemistry 26 (21): 6735–6742. doi:10.1021/bi00395a024. PMID 2447940. 
  2. ^ Jenne D (1991). "Homology of placental protein 11 and pea seed albumin 2 with vitronectin". Biochem. Biophys. Res. Commun. 176 (3): 1000–1006. doi:10.1016/0006-291X(91)90381-G. PMID 1710108. 
  3. ^ Rebbe NF, Tong BD, Finley EM, Hickman S (1991). "Identification of nucleotide pyrophosphatase/alkaline phosphodiesterase I activity associated with the mouse plasma cell differentiation antigen PC-1". Proc. Natl. Acad. Sci. U.S.A. 88 (12): 5192–5196. doi:10.1073/pnas.88.12.5192. PMC 51838. PMID 1647027. 
  4. ^ Gijsbers R, Ceulemans H, Bollen M (2003). "Functional characterization of the non-catalytic ectodomains of the nucleotide pyrophosphatase/phosphodiesterase NPP1". Biochem. J. 371 (Pt 2): 321–330. doi:10.1042/BJ20021943. PMC 1223305. PMID 12533192. 
  5. ^ Dyson HJ, Kamikubo Y, Kroon G, Curriden S, Neels JG, Churchill MJ, Dawson P, Jagielska A, Scheraga HA, Loskutoff DJ, De Guzman R, OBdziej S (2004). "Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin". Biochemistry 43 (21): 6519–6534. doi:10.1021/bi049647c. PMID 15157085. 
  6. ^ Carrell RW, Zhou A, Read RJ, Huntington JA, Pannu NS (2003). "How vitronectin binds PAI-1 to modulate fibrinolysis and cell migration". Nat. Struct. Biol. 10 (7): 541–544. doi:10.1038/nsb943. PMID 12808446. 

This article incorporates text from the public domain Pfam and InterPro IPR001212


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Somatomedin B domain Provide feedback

No Pfam abstract.

Literature references

  1. Patthy L; , J Mol Biol 1988;202:689-696.: 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. PUBMED:2459396 EPMC:2459396


External database links

This tab holds annotation information from the InterPro database.

InterPro entry 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].

Gene Ontology

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Domain organisation

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Alignments

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(73)
Full
(1147)
Representative proteomes NCBI
(1024)
Meta
(13)
RP15
(152)
RP35
(189)
RP55
(320)
RP75
(540)
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Format an alignment

  Seed
(73)
Full
(1147)
Representative proteomes NCBI
(1024)
Meta
(13)
RP15
(152)
RP35
(189)
RP55
(320)
RP75
(540)
Alignment:
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  Seed
(73)
Full
(1147)
Representative proteomes NCBI
(1024)
Meta
(13)
RP15
(152)
RP35
(189)
RP55
(320)
RP75
(540)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 73
Number in full: 1147
Average length of the domain: 45.40 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 10.31 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.1 23.1
Trusted cut-off 23.3 23.2
Noise cut-off 23.0 23.0
Model length: 44
Family (HMM) version: 12
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Species distribution

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Interactions

There is 1 interaction for this family. More...

Serpin

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Somatomedin_B domain has been found. There are 24 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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