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PR01922

Identifier
TNFACTORR5  [View Relations]  [View Alignment]  
Accession
PR01922
No. of Motifs
5
Creation Date
17-APR-2008
Title
Tumour necrosis factor receptor 5 signature
Database References

PDB; 1CDF; 1CZZ; 1D00; 1FLL; 1LB6
SCOP; 1CDF; 1CZZ; 1D00; 1FLL; 1LB6
CATH; 1CDF; 1CZZ; 1D00; 1FLL; 1LB6
MIM; 109535
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. VAN KOOTEN, C. AND BANCHEREAU, J.
CD40-CD40 ligand.
J.LEUKOC.BIOL. 67  2-17 (2000).

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 5 (also known as CD40 antigen) is expressed by a wide variety 
of cell types, including B lymphocytes, macrophages, dendritic cells, 
endothelial cells and epithelial cells. The receptor plays an important
role in T cell-mediated B lymphocyte activation [7].
 
TNFACTORR5 is a 5-element fingerprint that provides a signature for tumour
necrosis factor receptor 5. 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 areas that
characterise TNF receptor 5 but distinguish it from other TNF receptor
subtypes - motifs 1-3 reside within the extracellular N-terminal region;
and motifs 4 and 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 8 sequences was identified. Three partial 
matches were also found: Q6P2H9_HUMAN and A2A5L5_MOUSE are truncated human
and mouse receptors, respectively, which fail to match motifs 4 and 5; and
Q9DDD2_CHICK is a chicken TNF receptor 5 that fails to match motifs 1-3.
Summary Information
   8 codes involving  5 elements
0 codes involving 4 elements
2 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
588888
400000
322200
200011
12345
True Positives
Q4QQW2_RAT    TNR5_BOVIN    TNR5_CALJA    TNR5_CANFA    
TNR5_HORSE TNR5_HUMAN TNR5_MOUSE TNR5_PIG
True Positive Partials
Codes involving 3 elements
A2A5L5_MOUSE Q6P2H9_HUMAN
Codes involving 2 elements
Q9DDD2_CHICK
Sequence Titles
Q4QQW2_RAT  Tumor necrosis factor receptor superfamily, member 5 - Rattus norvegicus (Rat). 
TNR5_BOVIN Tumor necrosis factor receptor superfamily member 5 precursor (CD40L receptor) (B-cell surface antigen CD40) (CD40 antigen) - Bos taurus (Bovine).
TNR5_CALJA Tumor necrosis factor receptor superfamily member 5 precursor (CD40L receptor) (B-cell surface antigen CD40) (CD40 antigen) - Callithrix jacchus (Common marmoset).
TNR5_CANFA Tumor necrosis factor receptor superfamily member 5 precursor (CD40L receptor) (B-cell surface antigen CD40) (CD40 antigen) - Canis familiaris (Dog).
TNR5_HORSE Tumor necrosis factor receptor superfamily member 5 precursor (CD40L receptor) (B-cell surface antigen CD40) (CD40 antigen) - Equus caballus (Horse).
TNR5_HUMAN Tumor necrosis factor receptor superfamily member 5 precursor (CD40L receptor) (B-cell surface antigen CD40) (Bp50) (CD40 antigen) (CDw40) - Homo sapiens (Human).
TNR5_MOUSE Tumor necrosis factor receptor superfamily member 5 precursor (CD40L receptor) (B-cell surface antigen CD40) (Bp50) (CD40 antigen) - Mus musculus (Mouse).
TNR5_PIG Tumor necrosis factor receptor superfamily member 5 precursor (CD40L receptor) (B-cell surface antigen CD40) (CD40 antigen) - Sus scrofa (Pig).

A2A5L5_MOUSE CD40 antigen - Mus musculus (Mouse).
Q6P2H9_HUMAN CD40 protein - Homo sapiens (Human).

Q9DDD2_CHICK CD40-homologue - Gallus gallus (Chicken).
Scan History
SPTR55_38f 2  100  NSINGLE    
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
MVRLPLQCVLWGCLLT TNR5_HUMAN 1 1 -
MVSLPRLCALWGCLLT TNR5_MOUSE 1 1 -

Motif 2 width=15
Element Seqn Id St Int Rpt
KYCDPNLGLRVQQKG TNR5_HUMAN 81 64 -
RHCEPNQGLRVKKEG TNR5_MOUSE 81 64 -

Motif 3 width=14
Element Seqn Id St Int Rpt
ETDTICTCEEGWHC TNR5_HUMAN 98 2 -
ESDTVCTCKEGQHC TNR5_MOUSE 98 2 -

Motif 4 width=13
Element Seqn Id St Int Rpt
PVQETLHGCQPVT TNR5_HUMAN 250 138 -
PVQETLHGCQPVT TNR5_MOUSE 251 139 -

Motif 5 width=13
Element Seqn Id St Int Rpt
DGKESRISVQERQ TNR5_HUMAN 265 2 -
DGKESRISVQERQ TNR5_MOUSE 266 2 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
MVRLPLQCVLWGCLLT TNR5_HUMAN 1 1 -
MVRLPLQCLLWGCLLT TNR5_HORSE 1 1 -
MVRLPLKCLLWGCFLT TNR5_PIG 1 1 -
MFRLPLQCVLWGCLLS TNR5_CALJA 1 1 -
MVLLPLRCLFWGSLLT TNR5_CANFA 1 1 -
MVSLPRLCALWGCLLT TNR5_MOUSE 1 1 -
MVRLPLQCLFWGFFLT TNR5_BOVIN 1 1 -
MLPLPQLCALWGCLLT Q4QQW2_RAT 1 1 -

Motif 2 width=15
Element Seqn Id St Int Rpt
KYCDPNLGLRVQQKG TNR5_HUMAN 81 64 -
KYCDPNLGLQVQGTG TNR5_HORSE 81 64 -
KYCDPNLGLQVQREG TNR5_PIG 81 64 -
KYCDPNLGLRVQQEG TNR5_CALJA 81 64 -
KYCDPNLGLHVEKEG TNR5_CANFA 81 64 -
RHCEPNQGLRVKKEG TNR5_MOUSE 81 64 -
RYCNPNLGLRIQSEG TNR5_BOVIN 81 64 -
RHCELNQGLQVKKEG Q4QQW2_RAT 81 64 -

Motif 3 width=14
Element Seqn Id St Int Rpt
ETDTICTCEEGWHC TNR5_HUMAN 98 2 -
TTDATCICHEGQHC TNR5_HORSE 98 2 -
KTDTTCVCSEGHHC TNR5_PIG 98 2 -
VTDNICVCKEGRHC TNR5_CALJA 98 2 -
ETDTTCTCDEGLHC TNR5_CANFA 98 2 -
ESDTVCTCKEGQHC TNR5_MOUSE 98 2 -
NTDTTCVCVEGQHC TNR5_BOVIN 98 2 -
VSDTVCTCKEGQHC Q4QQW2_RAT 98 2 -

Motif 4 width=13
Element Seqn Id St Int Rpt
PVQETLHGCQPVT TNR5_HUMAN 250 138 -
PVQETLHGCQPVT TNR5_HORSE 253 141 -
PVQETLHWCQPVT TNR5_PIG 251 139 -
PVQETLHGCQPVA TNR5_CALJA 247 135 -
PVQETLHGCQPVT TNR5_CANFA 247 135 -
PVQETLHGCQPVT TNR5_MOUSE 251 139 -
PVQETLCWCQPVA TNR5_BOVIN 253 141 -
PVQETLHGCQPVA Q4QQW2_RAT 251 139 -

Motif 5 width=13
Element Seqn Id St Int Rpt
DGKESRISVQERQ TNR5_HUMAN 265 2 -
DGKESRISVQERQ TNR5_HORSE 268 2 -
DGKESRISVQERE TNR5_PIG 266 2 -
DGKESRISVQERQ TNR5_CALJA 262 2 -
DGKESRISVQERV TNR5_CANFA 262 2 -
DGKESRISVQERQ TNR5_MOUSE 266 2 -
DGKESRISVQERE TNR5_BOVIN 268 2 -
DGKESRISVQERQ Q4QQW2_RAT 266 2 -