Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

• HOME
• SETUP
• FAQ
• ABOUT
• GLOSSARY
• WHAT'S NEW
• FEEDBACK

Sema semaphorin domain

SMART accession number:	SM00630
Description:
Interpro abstract (IPR001627):	The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in a hepatocyte growth factor receptor, in SEX protein [(PUBMED:9875845)] and in viral proteins. CD100 (also called SEMA4D) is associated with PTPase and serine kinase activity. CD100 increases PMA, CD3 and CD2 induced T cell proliferation, increases CD45 induced T cell adhesion, induces B cell homotypic adhesion and down-regulates B cell expression of CD23. The Sema domain is characterised by a conserved set of cysteine residues, which form four disulphide bonds to stabilise the structure. The Sema domain fold is a variation of the beta propeller topology, with seven blades radially arranged around a central axis. Each blade contains a four- stranded (strands A to D) antiparallel beta sheet. The inner strand of each blade (A) lines the channel at the centre of the propeller, with strands B and C of the same repeat radiating outward, and strand D of the next repeat forming the outer edge of the blade. The large size of the Sema domain is not due to a single inserted domain but results from the presence of additional secondary structure elements inserted in most of the blades. The Sema domain uses a 'loop and hook' system to close the circle between the first and the last blades. The blades are constructed sequentially with an N-terminal beta- strand closing the circle by providing the outermost strand (D) of the seventh (C-terminal) blade. The beta-propeller is further stabilised by an extension of the N terminus, providing an additional, fifth beta-strand on the outer edge of blade 6 [(PUBMED:12925274), (PUBMED:12958590), (PUBMED:15167892)].
GO function:	protein binding (GO:0005515)
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 1328 Sema domains in 1326 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a Sema domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with Sema domain is also avaliable.

  Useful shortcuts: Expand all nodes or Collapse tree
  Go to specific node: Anopheles gambiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Takifugu rubripes

• Metabolism (metabolic pathways involving proteins which contain this domain)

• % proteins involved KEGG pathway ID Description 72.49 map04360 Axon guidance 3.93 map04520 Adherens junction 3.93 map05120 Epithelial cell signaling in Helicobacter pylori infection 3.93 map05210 Colorectal cancer 3.93 map04060 Cytokine-cytokine receptor interaction 3.93 map04510 Focal adhesion 3.93 map05211 Renal cell carcinoma 3.93 map05218 Melanoma 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 Sema domain which could be assigned to a KEGG orthologous group, and not all proteins containing Sema 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 Sema domains in PDB

  PDB code	Main view	Title
  1olz		The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of sema4d
  1q47		Structure of the semaphorin 3a receptor-binding module
  1shy		The crystal structure of hgf beta-chain in complex with the sema domain of the met receptor.
  2uzx		Structure of the human receptor tyrosine kinase met in complex with the listeria monocytogenes invasion protein inlb: crystal form i
  2uzy		Structure of the human receptor tyrosine kinase met in complex with the listeria monocytogenes invasion protein inlb: low resolution, crystal form ii

• Links (links to other resources describing this domain)

• INTERPRO	IPR001627

Send comments to Ivica Letunic