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PR01963

Identifier
TNFACTORR13B  [View Relations]  [View Alignment]  
Accession
PR01963
No. of Motifs
4
Creation Date
23-JUN-2009
Title
Tumour necrosis factor receptor 13B signature
Database References

PFAM; PF09305 TACI-CRD2
INTERPRO; IPR015384
PDB; 1XU1; 1XUT
SCOP; 1XU1; 1XUT
CATH; 1XU1; 1XUT
MIM; 604907
Literature References
1. ARMITAGE, R.
Tumor necrosis factor receptor superfamily members and their ligands.
CURR.OPIN.IMMUNOL. 6 407-413 (1994).
 
2. BANNER D., D'ARCY, A., JAMES, W., GENTZ, R., SCHOENFELD, H., BROGER, C.,
LOETSCHER, H. AND LESSLAUER, W.
Crystal structure of the soluble human 55 kD TNF receptor-human TNF-beta
complex: implications for TNF receptor activation.
CELL 73 431-445 (1993).
 
3. WU, H.
Assembly of post-receptor signaling complexes for the tumor necrosis factor
receptor superfamily.
ADV.PROTEIN CHEM. 68 225-279 (2004).
 
4. LOCKSLEY, R., KILLEEN, N. AND LENARDO, M.
The TNF and TNF Receptor Superfamilies: Integrating Mammalian Biology.
CELL 104 487-501 (2001).
 
5. GRAVESTEIN, L. AND BORST, J.
Tumor necrosis factor receptor family members in the immune system.
SEMIN.IMMUNOL. 10 423-434 (1998).
 
6. LOENEN, W.
D27 and (TNFR) relatives in the immune system: their role in health and
disease.
SEMIN.IMMUNOL. 10 417-422 (1998).
 
7. GROSS, J., JOHNSTON, J., MUDRI, S., ENSELMAN, R., DILLON, S., MADDEN, K.,
XU, W., PARRISH-NOVAK, J., FOSTER, D,, LOFTON-DAY, C., MOORE, M,, LITTAU, 
A., GROSSMAN, A., HAUGEN, H., FOLEY, K., BLUMBERG, H,, HARRISON, K., 
KINDSVOGEL, W. AND CLEGG C.
TACI and BCMA are receptors for a TNF homologue implicated in B-cell 
autoimmune disease.
NATURE 404 995-999 (2000).
 
8. CASTIGLI, E., WILSON, S., GARIBYAN, L., RACHID, R., BONILLA, F., 
SCHNEIDER, L. AND GEHA, R.
TACI is mutant in common variable immunodeficiency and IgA deficiency.
NAT.GENET. 37 829-834 (2005).

Documentation
The tumour necrosis factor (TNF) receptor (TNFR) superfamily comprises more
than 20 type-I transmembrane proteins. Family members are defined based on
similarity in their extracellular domain - a region that contains many
cysteine residues arranged in a specific repetitive pattern [1]. The
cysteines allow formation of an extended rod-like structure, responsible for
ligand binding [2].
 
Upon receptor activation, different intracellular signalling complexes are
assembled for different members of the TNFR superfamily, depending on their
intracellular domains and sequences [3]. Activation of TNFRs can therefore
induce a range of disparate effects, including cell proliferation,
differentiation, survival, or apoptotic cell death, depending upon the
receptor involved [4,5].
 
TNFRs are widely distributed and play important roles in many crucial
biological processes, such as lymphoid and neuronal development, innate and
adaptive immunity, and maintenance of cellular homeostasis [3]. Drugs that
manipulate their signalling have potential roles in the prevention and
treatment of many diseases, such as viral infections, coronary heart
disease, transplant rejection, and immune disease [6].
 
TNF receptor 13B (also known as transmembrane activator and CAML interactor 
(TACI)) functions as a receptor for B-cell activating factor (BAFF) [7].
Mutations in TNF receptor 13B cause common variable immunodeficiency (CVID)
and IgA deficiency [8].
 
TNFACTORR13B is a 4-element fingerprint that provides a signature for tumour
necrosis factor receptor 13B. The fingerprint was derived from an initial 
alignment of 3 sequences: the motifs were drawn from conserved regions in
the N- and C-terminal thirds of the alignment, focusing on those sections 
that characterise TNF receptor 13B but distinguish it from other TNF 
receptor subtypes - motifs 1, 2 and 3 lie within the extracellular
N-terminal region, and motif 4 resides within the intracellular C-terminal
region. Two iterations on SPTR57_40f were required to reach convergence, at
which point a true set comprising 6 sequences was identified. Three partial 
matches were also found, B4E0B0_HUMAN, Q32LX4_HUMAN and B7Z6V8_HUMAN, all of
which are translated human sequences that fail to match the full complement
of motifs.
Summary Information
   6 codes involving  4 elements
3 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
46666
31332
20000
1234
True Positives
A4Q912_CHICK  A5D8Y6_MOUSE  A5D8Y7_MOUSE  Q4ACX1_HUMAN  
TR13B_HUMAN TR13B_MOUSE
True Positive Partials
Codes involving 3 elements
B4E0B0_HUMAN B7Z6V8_HUMAN Q32LX4_HUMAN
Sequence Titles
A4Q912_CHICK TNFRSF13B protein - Gallus gallus (Chicken).  
A5D8Y6_MOUSE Tumor necrosis factor receptor superfamily, member 13b - Mus musculus (Mouse).
A5D8Y7_MOUSE Tumor necrosis factor receptor superfamily, member 13b - Mus musculus (Mouse).
Q4ACX1_HUMAN TACI (Tumor necrosis factor receptor superfamily, member 13B) (Tumor necrosis factor receptor superfamily, member 13B, isoform CRA_a) - Homo sapiens (Human).
TR13B_HUMAN Tumor necrosis factor receptor superfamily member 13B - Homo sapiens (Human).
TR13B_MOUSE Tumor necrosis factor receptor superfamily member 13B - Mus musculus (Mouse).

B4E0B0_HUMAN cDNA FLJ52819, highly similar to Tumor necrosis factor receptor superfamilymember 13B - Homo sapiens (Human).
B7Z6V8_HUMAN cDNA FLJ52770, highly similar to Tumor necrosis factor receptor superfamily member 13B - Homo sapiens (Human).
Q32LX4_HUMAN TNFRSF13B protein - Homo sapiens (Human).
Scan History
SPTR57_40f 2  300  NSINGLE    
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
MAMAFCPKDQYWD TR13B_MOUSE 1 1 -
VAMRSCPEEQYWD TR13B_HUMAN 29 29 -
AAVNNCTNQQYWD A4Q912_CHICK 9 9 -

Motif 2 width=11
Element Seqn Id St Int Rpt
INCRKEQGRYY TR13B_MOUSE 41 27 -
LSCRKEQGKFY TR13B_HUMAN 69 27 -
AVCNRRAGFYY A4Q912_CHICK 49 27 -

Motif 3 width=12
Element Seqn Id St Int Rpt
CDSTCTQHPQQC TR13B_MOUSE 61 9 -
CASICGQHPKQC TR13B_HUMAN 89 9 -
CSTVCGQHPKQC A4Q912_CHICK 69 9 -

Motif 4 width=12
Element Seqn Id St Int Rpt
QPVETCSFCFPE TR13B_MOUSE 189 116 -
EPVETCSFCFPE TR13B_HUMAN 225 124 -
EPVETCGFCFPG A4Q912_CHICK 188 107 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
MAMAFCPKDQYWD A5D8Y6_MOUSE 1 1 -
MAMAFCPKDQYWD TR13B_MOUSE 1 1 -
MAMAFCPKDQYWD A5D8Y7_MOUSE 1 1 -
VAMRSCPEEQYWD Q4ACX1_HUMAN 29 29 -
VAMRSCPEEQYWD TR13B_HUMAN 29 29 -
AAVNNCTNQQYWD A4Q912_CHICK 9 9 -

Motif 2 width=11
Element Seqn Id St Int Rpt
INCRKEQGRYY A5D8Y6_MOUSE 41 27 -
INCRKEQGRYY TR13B_MOUSE 41 27 -
INCRKEQGRYY A5D8Y7_MOUSE 41 27 -
LSCRKEQGKFY Q4ACX1_HUMAN 69 27 -
LSCRKEQGKFY TR13B_HUMAN 69 27 -
AVCNRRAGFYY A4Q912_CHICK 49 27 -

Motif 3 width=12
Element Seqn Id St Int Rpt
CDSTCTQHPQQC A5D8Y6_MOUSE 61 9 -
CDSTCTQHPQQC TR13B_MOUSE 61 9 -
CDSTCTQHPQQC A5D8Y7_MOUSE 61 9 -
CASICGQHPKQC Q4ACX1_HUMAN 89 9 -
CASICGQHPKQC TR13B_HUMAN 89 9 -
CSTVCGQHPKQC A4Q912_CHICK 69 9 -

Motif 4 width=12
Element Seqn Id St Int Rpt
QPVETCSFCFPE A5D8Y6_MOUSE 189 116 -
QPVETCSFCFPE TR13B_MOUSE 189 116 -
QPVETCSFCFPE A5D8Y7_MOUSE 189 116 -
EPVETCSFCFPE Q4ACX1_HUMAN 225 124 -
EPVETCSFCFPE TR13B_HUMAN 225 124 -
EPVETCGFCFPG A4Q912_CHICK 188 107 -