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PR01966

Identifier
TNFACTORR16  [View Relations]  [View Alignment]  
Accession
PR01966
No. of Motifs
4
Creation Date
25-JUN-2009
Title
Tumour necrosis factor receptor 16 signature
Database References

PDB; 1SG1; 3BUK; 1NGR
SCOP; 1SG1; 3BUK; 1NGR
CATH; 1SG1; 1NGR
MIM; 162010
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. CRAGNOLINI, A. AND FRIEDMAN, W.
The function of p75NTR in glia.
TRENDS NEUROSCI. 31 99-104 (2008).
 
8. NASSENSTEIN, C., KAMMERTOENS, T., VERES, T., UCKERT, W., SPIES, E., 
FUCHS, B., KRUG, N. AND BRAUN, A.
Neuroimmune crosstalk in asthma: dual role of the neurotrophin receptor 
p75NTR.
J.ALLERGY CLIN.IMMUNOL. 120 1089-1096 (2007).

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 16 (also known as nerve growth factor receptor (NGFR) and 
p75NTR)) acts as a low affinity receptor for neurotrophins. The receptor 
mediates a variety of contradictory cellular functions, including cell 
survival or apoptosis, promotion or inhibition of axonal growth, and
facilitation or attenuation of proliferation, depending on the cellular 
context [7]. The receptor may also play a role in inflammation, and has been
implicated in the pathogenesis of asthma [8].
 
TNFACTORR16 is a 4-element fingerprint that provides a signature for tumour
necrosis factor receptor 16. The fingerprint was derived from an initial
alignment of 6 sequences: the motifs were drawn from conserved regions in
the N-terminal half of the alignment, focusing on those sections that
characterise TNF receptor 16 but distinguish it from other TNF receptor
subtypes - all motifs lie in the extracellular N-terminal region. Two 
iterations on SPTR57_40f were required to reach convergence, at which point
a true set comprising 17 sequences was identified. Two partial matches were
also found, B6MU31_BRAFL and B4E096_HUMAN, which are lancelet and human 
translated sequences that fail to match motif 4, and motifs 1 and 2, 
respectively.
Summary Information
  17 codes involving  4 elements
1 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
417171717
31110
20011
1234
True Positives
A5PJV7_BOVIN  A9UGK7_CHICK  B2R961_HUMAN  Q32NM5_XENLA  
Q4KLX7_XENLA Q4RG40_TETNG Q66JK7_XENTR Q68Y16_XENLA
Q6JA22_XENLA Q8BYY1_MOUSE Q8CFT3_MOUSE Q9PRG7_XENLA
Q9PVD4_XENLA TNR16_CHICK TNR16_HUMAN TNR16_MOUSE
TNR16_RAT
True Positive Partials
Codes involving 3 elements
B6MU31_BRAFL
Codes involving 2 elements
B4E096_HUMAN
Sequence Titles
A5PJV7_BOVIN NGFR protein - Bos taurus (Bovine).           
A9UGK7_CHICK Low affinity neurotrophin p75 receptor - Gallus gallus (Chicken).
B2R961_HUMAN cDNA, FLJ94232, Homo sapiens nerve growth factor receptor (TNFR superfamily, member16) (NGFR), mRNA (Nerve growth factor receptor) (TNFR superfamily, member 16) - Homo sapiens (Human).
Q32NM5_XENLA LOC432338 protein - Xenopus laevis (African clawed frog).
Q4KLX7_XENLA LOC398134 protein - Xenopus laevis (African clawed frog).
Q4RG40_TETNG Chromosome 2 SCAF15106, whole genome shotgun sequence - Tetraodon nigroviridis (Green puffer).
Q66JK7_XENTR Ngfr protein - Xenopus tropicalis (Western clawed frog) (Silurana tropicalis).
Q68Y16_XENLA Neurotrophin receptor-related protein 1b - Xenopus laevis (African clawed frog).
Q6JA22_XENLA NRH - Xenopus laevis (African clawed frog).
Q8BYY1_MOUSE Putative uncharacterized protein - Mus musculus (Mouse).
Q8CFT3_MOUSE Nerve growth factor receptor (TNFR superfamily, member 16) - Mus musculus (Mouse).
Q9PRG7_XENLA P75 neurotrophin receptor a-2 (p75 neurotrophin receptor a-1) - Xenopus laevis (African clawed frog).
Q9PVD4_XENLA P75-like transmembrane protein fullback (Neurotrophin receptor-related protein 1a) - Xenopus laevis (African clawed frog).
TNR16_CHICK Tumor necrosis factor receptor superfamily member 16 - Gallus gallus (Chicken).
TNR16_HUMAN Tumor necrosis factor receptor superfamily member 16 - Homo sapiens (Human).
TNR16_MOUSE Tumor necrosis factor receptor superfamily member 16 - Mus musculus (Mouse).
TNR16_RAT Tumor necrosis factor receptor superfamily member 16 - Rattus norvegicus (Rat).

B6MU31_BRAFL Putative uncharacterized protein - Branchiostoma floridae (Florida lancelet) (Amphioxus).

B4E096_HUMAN cDNA FLJ51424, highly similar to Tumor necrosis factor receptor superfamilymember 16 - Homo sapiens (Human).
Scan History
SPTR57_40f 2  300  NSINGLE    
Initial Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
GEGVAQPCGAN TNR16_MOUSE 43 43 -
GEGVAQPCGAN TNR16_HUMAN 50 50 -
GEGVVQPCGVN TNR16_CHICK 42 42 -
GFGVTVPCGVS Q66JK7_XENTR 40 40 -
GFGVVVPCGDS Q4KLX7_XENLA 43 43 -
GDGVVTPCGDT Q4RG40_TETNG 103 103 -

Motif 2 width=12
Element Seqn Id St Int Rpt
SATEPCKPCTEC TNR16_MOUSE 71 17 -
SATEPCKPCTEC TNR16_HUMAN 78 17 -
SATEPCKPCTQC TNR16_CHICK 70 17 -
SATAKCQPCSTC Q66JK7_XENTR 68 17 -
SAKAKCQPCFTC Q4KLX7_XENLA 71 17 -
SHTEQCKPCTEC Q4RG40_TETNG 131 17 -

Motif 3 width=14
Element Seqn Id St Int Rpt
CSVCGVGSGLVFSC TNR16_MOUSE 118 35 -
CRVCEAGSGLVFSC TNR16_HUMAN 125 35 -
CSICEVGFGLMFPC TNR16_CHICK 117 35 -
CQVCSRGHGVVALC Q66JK7_XENTR 115 35 -
CQLCSKGHGVVSQC Q4KLX7_XENLA 118 35 -
CTMCPEGQGVLAGC Q4RG40_TETNG 178 35 -

Motif 4 width=10
Element Seqn Id St Int Rpt
DEANHVDPCL TNR16_MOUSE 149 17 -
DEANHVDPCL TNR16_HUMAN 156 17 -
DEANFVDPCL TNR16_CHICK 148 17 -
EVKSSESPCL Q66JK7_XENTR 146 17 -
EVKSSESPCL Q4KLX7_XENLA 149 17 -
DQESSWDPCI Q4RG40_TETNG 209 17 -
Final Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
GEGVAQPCGAN TNR16_RAT 51 51 -
GEGVAQPCGAN Q8BYY1_MOUSE 43 43 -
GEGVAQPCGAN TNR16_MOUSE 43 43 -
GEGVAQPCGAN Q8CFT3_MOUSE 53 53 -
GEGVAQPCGAN A5PJV7_BOVIN 52 52 -
GEGVAQPCGAN TNR16_HUMAN 50 50 -
GEGVAQPCGAN B2R961_HUMAN 50 50 -
GEGVVQPCGVN A9UGK7_CHICK 40 40 -
GEGVVQPCGVN TNR16_CHICK 42 42 -
GFGVAVPCGVS Q32NM5_XENLA 39 39 -
GFGVAVPCGVS Q6JA22_XENLA 41 41 -
GFGVAVPCGVS Q68Y16_XENLA 41 41 -
GFGVTVPCGVS Q66JK7_XENTR 40 40 -
GFGVVVPCGDS Q4KLX7_XENLA 43 43 -
GFGVVVPCGDS Q9PVD4_XENLA 43 43 -
GEGVIKRCGVN Q9PRG7_XENLA 40 40 -
GDGVVTPCGDT Q4RG40_TETNG 103 103 -

Motif 2 width=12
Element Seqn Id St Int Rpt
SATEPCKPCTEC TNR16_RAT 79 17 -
SATEPCKPCTEC Q8BYY1_MOUSE 71 17 -
SATEPCKPCTEC TNR16_MOUSE 71 17 -
SATEPCKPCTEC Q8CFT3_MOUSE 81 17 -
SATEPCKPCTEC A5PJV7_BOVIN 80 17 -
SATEPCKPCTEC TNR16_HUMAN 78 17 -
SATEPCKPCTEC B2R961_HUMAN 78 17 -
SATEPCKPCTQC A9UGK7_CHICK 68 17 -
SATEPCKPCTQC TNR16_CHICK 70 17 -
SATAKCQLCSPC Q32NM5_XENLA 67 17 -
SATAKCQLCSPC Q6JA22_XENLA 69 17 -
SATAKCQLCSPC Q68Y16_XENLA 69 17 -
SATAKCQPCSTC Q66JK7_XENTR 68 17 -
SAKAKCQPCFTC Q4KLX7_XENLA 71 17 -
SAKAKCQPCFTC Q9PVD4_XENLA 71 17 -
SHTEACKPCTEC Q9PRG7_XENLA 68 17 -
SHTEQCKPCTEC Q4RG40_TETNG 131 17 -

Motif 3 width=14
Element Seqn Id St Int Rpt
CSVCEVGSGLVFSC TNR16_RAT 126 35 -
CSVCGVGSGLVFSC Q8BYY1_MOUSE 118 35 -
CSVCGVGSGLVFSC TNR16_MOUSE 118 35 -
CSVCGVGSGLVFSC Q8CFT3_MOUSE 128 35 -
CRVCEAGSGLVFSC A5PJV7_BOVIN 127 35 -
CRVCEAGSGLVFSC TNR16_HUMAN 125 35 -
CRVCEAGSGLVFSC B2R961_HUMAN 125 35 -
CSICEVGFGLMFPC A9UGK7_CHICK 115 35 -
CSICEVGFGLMFPC TNR16_CHICK 117 35 -
CQLCPKGQGVVSFC Q32NM5_XENLA 113 34 -
CQLCPKGQGVVSFC Q6JA22_XENLA 115 34 -
CQLCPKGQGVVSFC Q68Y16_XENLA 115 34 -
CQVCSRGHGVVALC Q66JK7_XENTR 115 35 -
CQLCSKGHGVVSQC Q4KLX7_XENLA 118 35 -
CQLCSKGHGVVSQC Q9PVD4_XENLA 118 35 -
CKSCPEGFGMMMSC Q9PRG7_XENLA 115 35 -
CTMCPEGQGVLAGC Q4RG40_TETNG 178 35 -

Motif 4 width=10
Element Seqn Id St Int Rpt
DEANHVDPCL TNR16_RAT 157 17 -
DEANHVDPCL Q8BYY1_MOUSE 149 17 -
DEANHVDPCL TNR16_MOUSE 149 17 -
DEANHVDPCL Q8CFT3_MOUSE 159 17 -
DEANHVDPCL A5PJV7_BOVIN 158 17 -
DEANHVDPCL TNR16_HUMAN 156 17 -
DEANHVDPCL B2R961_HUMAN 156 17 -
DEANFVDPCL A9UGK7_CHICK 146 17 -
DEANFVDPCL TNR16_CHICK 148 17 -
EVKSRESPCL Q32NM5_XENLA 144 17 -
EVKSRESPCL Q6JA22_XENLA 146 17 -
EVKSRESPCL Q68Y16_XENLA 146 17 -
EVKSSESPCL Q66JK7_XENTR 146 17 -
EVKSSESPCL Q4KLX7_XENLA 149 17 -
EVKSSESPCL Q9PVD4_XENLA 149 17 -
DEDNDRDPCL Q9PRG7_XENLA 146 17 -
DQESSWDPCI Q4RG40_TETNG 209 17 -