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PR01920

Identifier
TNFACTORR3  [View Relations]  [View Alignment]  
Accession
PR01920
No. of Motifs
5
Creation Date
17-APR-2008
Title
Tumour necrosis factor receptor 3 signature
Database References

PDB; 1RF3
SCOP; 1RF3
CATH; 1RF3
MIM; 600979
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. VANARSDALE, T., VANARSDALE, S., FORCE, W., WALTER, B., MOSIALOS, G., 
KIEF, E., REED, J. AND WARE, C.
Lymphotoxin-beta receptor signaling complex: Role of tumor necrosis factor 
receptor-associated factor 3 recruitment in cell death and activation of 
nuclear factor B.
PROC.NATL.ACAD.SCI.U.S.A. 94 2460-2465 (1997).

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 3 (also known as lymphotoxin-beta receptor) acts as a receptor
for the heterotrimer of lymphotoxin-alpha and beta, and also for the TNF 
ligand LIGHT. Activation of the receptor promotes apoptosis via recruitment
of TNFR-associated factor 3 (TRAF3) [7]. 
 
TNFACTORR3 is a 5-element fingerprint that provides a signature for tumour 
necrosis factor receptor 3. The fingerprint was derived from an initial 
alignment of 2 sequences: the motifs were drawn from conserved regions 
spanning virtually the full alignment length, focusing on those sections
that characterise TNF receptor 3 but distinguish it from other TNF receptor 
subtypes - motif 1 resides within the extracellular N-terminal region; 
motif 2 spans part of the transmembrane domain and part of the intracellular
C-terminal region; and motifs 3-5 lie within the intracellular C-terminal
region. Two iterations on SPTR55_38f were required to reach convergence, at
which point a true set comprising 6 sequences was identified.
Summary Information
6 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
566666
400000
300000
200000
12345
True Positives
A6QQ46_BOVIN  Q3UK82_MOUSE  Q5RDW2_PONPY  Q5U2S8_RAT    
TNR3_HUMAN TNR3_MOUSE
Sequence Titles
A6QQ46_BOVIN LTBR protein - Bos taurus (Bovine).           
Q3UK82_MOUSE TIB-55 BB88 cDNA, RIKEN full-length enriched library, clone:I730007F13 product:lymphotoxin B receptor, full insert sequence - Mus musculus (Mouse).
Q5RDW2_PONPY Putative uncharacterized protein DKFZp469N1737 - Pongo pygmaeus (Orangutan).
Q5U2S8_RAT Lymphotoxin B receptor - Rattus norvegicus (Rat).
TNR3_HUMAN Tumor necrosis factor receptor superfamily member 3 precursor (Lymphotoxin-beta receptor) (Tumor necrosis factor receptor 2-related protein) (Tumor necrosis factor C receptor) - Homo sapiens (Human).
TNR3_MOUSE Tumor necrosis factor receptor superfamily member 3 precursor (Lymphotoxin-beta receptor) - Mus musculus (Mouse).
Scan History
SPTR55_38f 2  300  NSINGLE    
Initial Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
PYRIENQTCWDQDKEYYEP TNR3_MOUSE 35 35 -
PYASENQTCRDQEKEYYEP TNR3_HUMAN 35 35 -

Motif 2 width=12
Element Seqn Id St Int Rpt
ACAWMRHPSLCR TNR3_MOUSE 241 187 -
SCIWKSHPSLCR TNR3_HUMAN 245 191 -

Motif 3 width=14
Element Seqn Id St Int Rpt
FPDLAEPLLPMSGD TNR3_MOUSE 279 26 -
FPDLVQPLLPISGD TNR3_HUMAN 287 30 -

Motif 4 width=25
Element Seqn Id St Int Rpt
AHGANGIHVTGGSVTVTGNIYIYNG TNR3_MOUSE 334 41 -
AHGTNGIHVTGGSMTITGNIYIYNG TNR3_HUMAN 342 41 -

Motif 5 width=17
Element Seqn Id St Int Rpt
EDGKAWHLAETETLGCQ TNR3_MOUSE 397 38 -
EDGKAWHLAETEHCGAT TNR3_HUMAN 405 38 -
Final Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
PYRIENQTCWDQDKEYYEP Q3UK82_MOUSE 35 35 -
PYRIENQTCWDQDKEYYEP TNR3_MOUSE 35 35 -
PYASENQTCRDQEKEYYEP TNR3_HUMAN 35 35 -
PYGSENQTCRDQEKEYYEP Q5RDW2_PONPY 35 35 -
PYRIENQTCWDPDKEYYEP Q5U2S8_RAT 35 35 -
PYHTENQSCGDQEKEYYES A6QQ46_BOVIN 42 42 -

Motif 2 width=12
Element Seqn Id St Int Rpt
ACAWMRHPSLCR Q3UK82_MOUSE 241 187 -
ACAWMRHPSLCR TNR3_MOUSE 241 187 -
SCIWKSHPSLCR TNR3_HUMAN 245 191 -
ACIWKSHPSLCR Q5RDW2_PONPY 245 191 -
ACAWMRHPSLCR Q5U2S8_RAT 242 188 -
VYTWKSHPSLCR A6QQ46_BOVIN 250 189 -

Motif 3 width=14
Element Seqn Id St Int Rpt
FPDLAEPLLPMSGD Q3UK82_MOUSE 279 26 -
FPDLAEPLLPMSGD TNR3_MOUSE 279 26 -
FPDLVQPLLPISGD TNR3_HUMAN 287 30 -
FPDLVKPLLPISGD Q5RDW2_PONPY 287 30 -
FRDLAEPLLPMSGD Q5U2S8_RAT 280 26 -
VPDLVKPLLPAPGD A6QQ46_BOVIN 292 30 -

Motif 4 width=25
Element Seqn Id St Int Rpt
AHGANGIHVTGGSVTVTGNIYIYNG Q3UK82_MOUSE 334 41 -
AHGANGIHVTGGSVTVTGNIYIYNG TNR3_MOUSE 334 41 -
AHGTNGIHVTGGSMTITGNIYIYNG TNR3_HUMAN 342 41 -
AHGTNGIHVTGGSMTITGNIYIYNG Q5RDW2_PONPY 342 41 -
AHGANGIHVTGGSVTVTGNIYIYNG Q5U2S8_RAT 335 41 -
APGTNGIHVTGGSVTVTGNIYIYNG A6QQ46_BOVIN 347 41 -

Motif 5 width=17
Element Seqn Id St Int Rpt
EDGKAWHLAETETLGCQ Q3UK82_MOUSE 397 38 -
EDGKAWHLAETETLGCQ TNR3_MOUSE 397 38 -
EDGKAWHLAETEHCGAT TNR3_HUMAN 405 38 -
EDGKAWHLAETEHCGAT Q5RDW2_PONPY 405 38 -
EDGKAWHLAETETLGCQ Q5U2S8_RAT 398 38 -
EDGKAWHLAETETLGCY A6QQ46_BOVIN 410 38 -