WORKLIST ENTRIES (1):

TNFACTORR9 View alignment       Tumour necrosis factor receptor 9 signature
 Type of fingerprint: COMPOUND with 3  elements
Links:
   PRINTS; PR01918 TNFACTORR1A; PR01919 TNFACTORR1B; PR01920 TNFACTORR3
   PRINTS; PR01921 TNFACTORR4; PR01922 TNFACTORR5; PR01680 TNFACTORR6
   PRINTS; PR01960 TNFACTORR7; PR01923 TNFACTORR8; PR01956 TNFACTORR10
   PRINTS; PR01961 TNFACTORR11; PR01962 TNFACTORR12; PR01963 TNFACTORR13B
   PRINTS; PR01964 TNFACTORR13C; PR01965 TNFACTORR14; PR01966 TNFACTORR16
   PRINTS; PR01967 TNFACTORR17; PR01968 TNFACTORR18; PR01969 TNFACTORR19
   PRINTS; PR01970 TNFACTORR19l; PR01971 TNFACTORR21; PR01972 TNFACTORR25
   PRINTS; PR01973 TNFACTORR27
   PRINTS; PR01974 TNFACTORR11A; PR01975 TNFACTORR11B
   PDB; 1D0J 3Dinfo
   SCOP; 1D0J
   CATH; 1D0J
   MIM; 602250

 Creation date 23-APR-2008

   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).

   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 FINGERPRINT INDEX
  
    3|   7    7    7  
    2|   0    3    3  
   --+----------------
     |   1    2    3  

True positives..
 Q3U3R1_MOUSE   TNR9_MOUSE     TNR9_HUMAN     A9YYE7_MACFA   
 Q3ZC74_BOVIN   Q4V895_RAT     Q4W8J3_RAT     
Subfamily:  Codes involving 2 elements
 Subfamily True positives..
 A9YYF0_MACFA   A9YYF1_MACFA   Q8R037_MOUSE   


  PROTEIN TITLES
   Q3U3R1_MOUSE     NOD-derived CD11c +ve dendritic cells cDNA, RIKEN full-lengt
   TNR9_MOUSE       Tumor necrosis factor receptor superfamily member 9 precurso
   TNR9_HUMAN       Tumor necrosis factor receptor superfamily member 9 precurso
   A9YYE7_MACFA     CD137 - Macaca fascicularis (Crab eating macaque) (Cynomolgu
   Q3ZC74_BOVIN     Similar to tumor necrosis factor receptor superfamily, membe
   Q4V895_RAT       Similar to T-cell antigen 4-1BB-mouse - Rattus norvegicus (R
   Q4W8J3_RAT       4-1BB homolog - Rattus norvegicus (Rat).
 
   A9YYF0_MACFA     CD137 variant - Macaca fascicularis (Crab eating macaque) (C
   A9YYF1_MACFA     CD137 variant - Macaca fascicularis (Crab eating macaque) (C
   Q8R037_MOUSE     Tumor necrosis factor receptor superfamily, member 9 (Secret

SCAN HISTORY SPTR55_38f 2 300 NSINGLE INITIAL MOTIF SETS TNFACTORR91 Length of motif = 14 Motif number = 1 Tumour necrosis factor receptor 9 motif I - 1 PCODE ST INT IFITLLFSVLKWIR TNR9_MOUSE 202 202 FFLTLRFSVVKRGR TNR9_HUMAN 204 204 TNFACTORR92 Length of motif = 15 Motif number = 2 Tumour necrosis factor receptor 9 motif II - 1 PCODE ST INT IFKQPFKKTTGAAQE TNR9_MOUSE 221 5 IFKQPFMRPVQTTQE TNR9_HUMAN 223 5 TNFACTORR93 Length of motif = 11 Motif number = 3 Tumour necrosis factor receptor 9 motif III - 1 PCODE ST INT DACSCRCPQEE TNR9_MOUSE 237 1 DGCSCRFPEEE TNR9_HUMAN 239 1 FINAL MOTIF SETS TNFACTORR91 Length of motif = 14 Motif number = 1 Tumour necrosis factor receptor 9 motif I - 2 PCODE ST INT 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 TNFACTORR92 Length of motif = 15 Motif number = 2 Tumour necrosis factor receptor 9 motif II - 2 PCODE ST INT 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 TNFACTORR93 Length of motif = 11 Motif number = 3 Tumour necrosis factor receptor 9 motif III - 2 PCODE ST INT 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

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