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PR01961

Identifier
TNFACTORR11  [View Relations]  [View Alignment]  
Accession
PR01961
No. of Motifs
3
Creation Date
25-JUN-2009
Title
Tumour necrosis factor receptor 11 signature
Database References
PRINTS; PR01974 TNFACTORR11A; PR01975 TNFACTORR11B
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. NAKAGAWA, N., KINOSAKI, M., YAMAGUCHI, K., SHIMA, N., YASUDA, H.,
YANO, K., MORINAGA, T. AND HIGASHIO, K.
RANK is the essential signaling receptor for osteoclast differentiation 
factor in osteoclastogenesis.
BIOCHEM.BIOPHYS.RES.COMMUN. 253 395-400 (1998).
 
8. HOFBAUER, L. AND HEUFELDER, A.
Role of receptor activator of nuclear factor-kappaB ligand and 
osteoprotegerin in bone cell biology.
J.MOL.MED. 79 243-253 (2001).

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 receptors 11A and 11B mediate the effects of receptor activator for 
NF-kappa-B ligand (RANKL), an essential osteoclast regulatory factor. The 
receptors have opposing effects - activation of TNF receptor 11A by RANKL 
promotes osteoclast differentiation [7], while TNF receptor 11B acts as a 
soluble decoy receptor for the ligand, thus inhibiting differentiation [8].
 
TNFACTORR11 is a 3-element fingerprint that provides a signature for tumour 
necrosis factor receptor 11 subtypes A and B. The fingerprint was derived 
from an initial alignment of 10 sequences: the motifs were drawn from 
conserved regions in the N-terminal two thirds of the alignment, focusing on
those sections that characterise TNF receptors 11A and B but distinguish
them from other TNF receptor subtypes. A single iteration on SPTR57_40f was 
required to reach convergence, no further sequences being identified beyond
the starting set.
Summary Information
10 codes involving  3 elements
0 codes involving 2 elements
Composite Feature Index
3101010
2000
123
True Positives
A5D7R1_BOVIN  Q3UK97_MOUSE  Q4F9K2_CHICK  Q6GLN3_XENLA  
Q6PI12_MOUSE TNR11_HUMAN TNR11_MOUSE TR11B_HUMAN
TR11B_MOUSE TR11B_RAT
Sequence Titles
A5D7R1_BOVIN TNFRSF11B protein - Bos taurus (Bovine).      
Q3UK97_MOUSE Putative uncharacterized protein - Mus musculus (Mouse).
Q4F9K2_CHICK OPG - Gallus gallus (Chicken).
Q6GLN3_XENLA MGC84670 protein - Xenopus laevis (African clawed frog).
Q6PI12_MOUSE Tumor necrosis factor receptor superfamily, member 11b (Osteoprotegerin) - Mus musculus (Mouse).
TNR11_HUMAN Tumor necrosis factor receptor superfamily member 11A - Homo sapiens (Human).
TNR11_MOUSE Tumor necrosis factor receptor superfamily member 11A - Mus musculus (Mouse).
TR11B_HUMAN Tumor necrosis factor receptor superfamily member 11B - Homo sapiens (Human).
TR11B_MOUSE Tumor necrosis factor receptor superfamily member 11B - Mus musculus (Mouse).
TR11B_RAT Tumor necrosis factor receptor superfamily member 11B - Rattus norvegicus (Rat).
Scan History
SPTR57_40f 1  300  NSINGLE    
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
YTDSWHTSDECV Q3UK97_MOUSE 70 70 -
YTDSWHTSDECV TR11B_RAT 70 70 -
YTDSWHTSDECV TR11B_MOUSE 70 70 -
YTDSWHTSDECV Q6PI12_MOUSE 70 70 -
YTDSWHTSDECL TR11B_HUMAN 70 70 -
YTDTWHTSDECL A5D7R1_BOVIN 70 70 -
YAEDWNSNDECQ Q4F9K2_CHICK 70 70 -
YLDTWNEEDKCL TNR11_MOUSE 77 77 -
YLDSWNEEDKCL TNR11_HUMAN 76 76 -
YNDRWNSNTECQ Q6GLN3_XENLA 69 69 -

Motif 2 width=17
Element Seqn Id St Int Rpt
GLLLIQKGNATHDNVCS Q3UK97_MOUSE 170 88 -
GLLLIQKGNATHDNVCS TR11B_RAT 170 88 -
GLLLIQKGNATHDNVCS TR11B_MOUSE 170 88 -
GLLLIQKGNATHDNVCS Q6PI12_MOUSE 170 88 -
GLLLTQKGNATHDNICS TR11B_HUMAN 170 88 -
GLLLTQKGNATHDNICS A5D7R1_BOVIN 170 88 -
GFKTALKGNAVRDNICQ Q4F9K2_CHICK 170 88 -
GKLEAHQGTTESDVVCS TNR11_MOUSE 180 91 -
GKRVEHHGTEKSDAVCS TNR11_HUMAN 179 91 -
GIKVAYQGDSDHDTLCQ Q6GLN3_XENLA 169 88 -

Motif 3 width=13
Element Seqn Id St Int Rpt
WLSVLVDSLPGTK Q3UK97_MOUSE 219 32 -
WLSVLVDSLPGTK TR11B_RAT 219 32 -
WLSVLVDSLPGTK TR11B_MOUSE 219 32 -
WLSVLVDSLPGTK Q6PI12_MOUSE 219 32 -
WLSVLVDNLPGTK TR11B_HUMAN 219 32 -
WLSVLVDNLPGTK A5D7R1_BOVIN 220 33 -
WLNTLADNLPGTK Q4F9K2_CHICK 220 33 -
WVNDACSSLSGNK TNR11_MOUSE 250 53 -
WINEACGRLSGDK TNR11_HUMAN 249 53 -
WLTAIAQRPPSTM Q6GLN3_XENLA 210 24 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
YTDSWHTSDECV Q3UK97_MOUSE 70 70 -
YTDSWHTSDECV TR11B_RAT 70 70 -
YTDSWHTSDECV TR11B_MOUSE 70 70 -
YTDSWHTSDECV Q6PI12_MOUSE 70 70 -
YTDSWHTSDECL TR11B_HUMAN 70 70 -
YTDTWHTSDECL A5D7R1_BOVIN 70 70 -
YAEDWNSNDECQ Q4F9K2_CHICK 70 70 -
YLDTWNEEDKCL TNR11_MOUSE 77 77 -
YLDSWNEEDKCL TNR11_HUMAN 76 76 -
YNDRWNSNTECQ Q6GLN3_XENLA 69 69 -

Motif 2 width=17
Element Seqn Id St Int Rpt
GLLLIQKGNATHDNVCS Q3UK97_MOUSE 170 88 -
GLLLIQKGNATHDNVCS TR11B_RAT 170 88 -
GLLLIQKGNATHDNVCS TR11B_MOUSE 170 88 -
GLLLIQKGNATHDNVCS Q6PI12_MOUSE 170 88 -
GLLLTQKGNATHDNICS TR11B_HUMAN 170 88 -
GLLLTQKGNATHDNICS A5D7R1_BOVIN 170 88 -
GFKTALKGNAVRDNICQ Q4F9K2_CHICK 170 88 -
GKLEAHQGTTESDVVCS TNR11_MOUSE 180 91 -
GKRVEHHGTEKSDAVCS TNR11_HUMAN 179 91 -
GIKVAYQGDSDHDTLCQ Q6GLN3_XENLA 169 88 -

Motif 3 width=13
Element Seqn Id St Int Rpt
WLSVLVDSLPGTK Q3UK97_MOUSE 219 32 -
WLSVLVDSLPGTK TR11B_RAT 219 32 -
WLSVLVDSLPGTK TR11B_MOUSE 219 32 -
WLSVLVDSLPGTK Q6PI12_MOUSE 219 32 -
WLSVLVDNLPGTK TR11B_HUMAN 219 32 -
WLSVLVDNLPGTK A5D7R1_BOVIN 220 33 -
WLNTLADNLPGTK Q4F9K2_CHICK 220 33 -
WVNDACSSLSGNK TNR11_MOUSE 250 53 -
WINEACGRLSGDK TNR11_HUMAN 249 53 -
WLTAIAQRPPSTM Q6GLN3_XENLA 210 24 -