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PR01924

Identifier
TNFACTORR9  [View Relations]  [View Alignment]  
Accession
PR01924
No. of Motifs
3
Creation Date
23-APR-2008
Title
Tumour necrosis factor receptor 9 signature
Database References

PDB; 1D0J
SCOP; 1D0J
CATH; 1D0J
MIM; 602250
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. SCHWARZ, H., BLANCO, F., VON KEMPIS, J., VALBRACHT, J. AND LOTZ, M.
ILA, a member of the human nerve growth factor/tumor necrosis factor 
receptor family, regulates T-lymphocyte proliferation and survival.
BLOOD 87 2839-2845 (1996).

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 9 (also known as ILA and CD137 antigen) is expressed by
activated T and B lymphocytes and monocytes. Stimulation of the receptor
inhibits proliferation of activated T lymphocytes and induces programmed 
cell death [7].
 
TNFACTORR9 is a 3-element fingerprint that provides a signature for tumour
necrosis factor receptor 9. The fingerprint was derived from an initial
alignment of 2 sequences: the motifs were drawn from conserved regions in 
the C-terminal half of the alignment, focusing on those sections that
characterise TNF receptor 9 but distinguish it from other TNF receptor
subtypes - motif 1 lies partially in the transmembrane domain and partially
within the C-terminal cytoplasmic region; and motifs 2 and 3 reside within
the C-terminal cytoplasmic region. Two iterations on SPTR55_38f were
required to reach convergence, at which point a true set comprising 7 
sequences was identified. Three partial matches were also found, all
of which fail to match motif 1: Q8R037_MOUSE is a translated cDNA from
mouse; and A9YYF0_MACFA and A9YYF1_MACFA are receptor variants from crab- 
eating macaque.
Summary Information
   7 codes involving  3 elements
3 codes involving 2 elements
Composite Feature Index
3777
2033
123
True Positives
A9YYE7_MACFA  Q3U3R1_MOUSE  Q3ZC74_BOVIN  Q4V895_RAT    
Q4W8J3_RAT TNR9_HUMAN TNR9_MOUSE
True Positive Partials
Codes involving 2 elements
A9YYF0_MACFA A9YYF1_MACFA Q8R037_MOUSE
Sequence Titles
A9YYE7_MACFA CD137 - Macaca fascicularis (Crab eating macaque) (Cynomolgus monkey). 
Q3U3R1_MOUSE NOD-derived CD11c +ve dendritic cells cDNA, RIKEN full-length enriched library, clone:F630101J18 product:tumor necrosis factor receptor superfamily, member 9, full insert sequence (Tumor necrosis factor receptor superfamily, member 9) (CD137 antigen precursor) - Mus musculus (Mouse).
Q3ZC74_BOVIN Similar to tumor necrosis factor receptor superfamily, member 9 - Bos taurus (Bovine).
Q4V895_RAT Similar to T-cell antigen 4-1BB-mouse - Rattus norvegicus (Rat).
Q4W8J3_RAT 4-1BB homolog - Rattus norvegicus (Rat).
TNR9_HUMAN Tumor necrosis factor receptor superfamily member 9 precursor (4-1BB ligand receptor) (T-cell antigen 4-1BB homolog) (T-cell antigen ILA) (CD137 antigen) (CDw137) - Homo sapiens (Human).
TNR9_MOUSE Tumor necrosis factor receptor superfamily member 9 precursor (4-1BB ligand receptor) (T-cell antigen 4-1BB) (CD137 antigen) - Mus musculus (Mouse).

A9YYF0_MACFA CD137 variant - Macaca fascicularis (Crab eating macaque) (Cynomolgus monkey).
A9YYF1_MACFA CD137 variant - Macaca fascicularis (Crab eating macaque) (Cynomolgus monkey).
Q8R037_MOUSE Tumor necrosis factor receptor superfamily, member 9 (Secreted CD137 antigen precursor) - Mus musculus (Mouse).
Scan History
SPTR55_38f 2  300  NSINGLE    
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
IFITLLFSVLKWIR TNR9_MOUSE 202 202 -
FFLTLRFSVVKRGR TNR9_HUMAN 204 204 -

Motif 2 width=15
Element Seqn Id St Int Rpt
IFKQPFKKTTGAAQE TNR9_MOUSE 221 5 -
IFKQPFMRPVQTTQE TNR9_HUMAN 223 5 -

Motif 3 width=11
Element Seqn Id St Int Rpt
DACSCRCPQEE TNR9_MOUSE 237 1 -
DGCSCRFPEEE TNR9_HUMAN 239 1 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
IFITLLFSVLKWIR Q3U3R1_MOUSE 202 202 -
IFITLLFSVLKWIR TNR9_MOUSE 202 202 -
FFLTLRFSVVKRGR TNR9_HUMAN 204 204 -
FFLVLRFSVVKRSR A9YYE7_MACFA 203 203 -
SFLVLRFSVIKQGR Q3ZC74_BOVIN 203 203 -
IFIILWFSVPKWLR Q4V895_RAT 204 204 -
IFIILWFSVPKWLR Q4W8J3_RAT 204 204 -

Motif 2 width=15
Element Seqn Id St Int Rpt
IFKQPFKKTTGAAQE Q3U3R1_MOUSE 221 5 -
IFKQPFKKTTGAAQE TNR9_MOUSE 221 5 -
IFKQPFMRPVQTTQE TNR9_HUMAN 223 5 -
IFKQPFMRPVQTTQE A9YYE7_MACFA 222 5 -
IFKQPFMRPVQTAQE Q3ZC74_BOVIN 222 5 -
IFKQPFKKAVRTAQE Q4V895_RAT 223 5 -
IFKQPFKKAVRTAQE Q4W8J3_RAT 223 5 -

Motif 3 width=11
Element Seqn Id St Int Rpt
DACSCRCPQEE Q3U3R1_MOUSE 237 1 -
DACSCRCPQEE TNR9_MOUSE 237 1 -
DGCSCRFPEEE TNR9_HUMAN 239 1 -
DGCSCRFPEEE A9YYE7_MACFA 238 1 -
DACSCRFPEEE Q3ZC74_BOVIN 238 1 -
DACSCRFPEEE Q4V895_RAT 239 1 -
DACSCRFPEEE Q4W8J3_RAT 239 1 -