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PR01265

Identifier
LINKMODULE  [View Relations]  [View Alignment]  
Accession
PR01265
No. of Motifs
4
Creation Date
17-NOV-1999
Title
Link module signature
Database References

PROSITE; PS01241 LINK
BLOCKS; BL01241
PFAM; PF00193 Xlink
PDB; 1TSG
SCOP; 1TSG
CATH; 1TSG
Literature References
1. BARTA, E., DEAK, F. AND KISS, I. 
Evolution of the hyaluronan-binding module of link protein. 
BIOCHEM.J. 292 947-949 (1993). 
 
2. KOHDA, D., MORTON, C.J., PARKAR, A.A., HATANAKA, H., INAGAKI, F.M., 
CAMPBELL, I.D. AND DAY A.J.
Solution structure of the link module: a hyaluronan-binding domain involved
in extracellular matrix stability and cell migration.
CELL 86 767-775 (1996). 
 
3. BRISSET, N.C. AND PERKINS, S.J. 
The protein fold of the hyaluronate-binding proteoglycan tandem repeat 
domain of link protein, aggrecan and CD44 is similar to that of the C-type
lectin superfamily.
FEBS LETT. 388 211-216 (1996). 

Documentation
The link module (also known as HABM (HA binding module) or PTR (proteoglycan
tandem repeat) is an approximately 100 amino acid long hyaluronic acid-
binding domain found in vertebrate proteins involved in assembling the
extracellular matrix and in cell adhesion and migration [1-3]. The structure
consists of two alpha-helices and two short anti-parallel beta-strands built 
around a hydrophobic core [2]. The module contains four conserved cysteines 
involved in two disulphide bridges, as illustrated schematically below:
 
                            +----------+
                            |          |
            xxxxCxxxxxxxxxxxCxxxxxxxxxxCxxxxxxxxxxxxxxxCxxxxx
                |                                      |
                +--------------------------------------+
 
Proteins containing link modules include the proteoglycans aggrecan, 
brevican, neurocan and versican, and the cartilage link protein, each of
which contain two modules; tumor necrosis factor-inducible protein TSG-6 
and CD44 cell surface antigen, which each contain a single module (that in 
CD44 being at the N-terminus).
 
LINKMODULE is a 4-element fingerprint that provides a signature for the 
link module. The fingerprint was derived from an initial alignment of 5 
sequences: the motifs were drawn from strategically selected conserved
regions spanning the full alignment length - motif 1 encodes the N-terminal
helical region and first conserved cysteine residue; motif 2 spans the 
region flanking the second conserved Cys; motif 3 includes the region
preceding the third conserved Cys; and motif 4 is centred on the short
C-terminal beta-strand and fourth conserved Cys. Two iterations on
SPTR37_10f were required to reach convergence, at which point a true
set comprising 41 sequences was identified.
Summary Information
41 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
441414141
30000
20000
1234
True Positives
CD44_BOVIN    CD44_CRIGR    CD44_HORSE    CD44_HUMAN    
CD44_MESAU CD44_MOUSE CD44_PAPHA CD44_RAT
O08779 O08859 O14594 O70509
O77609 O77610 O77611 O77612
O88564 P79787 PGCA_BOVIN PGCA_CHICK
PGCA_HUMAN PGCA_MOUSE PGCA_RAT PGCB_BOVIN
PGCB_MOUSE PGCB_RAT PGCN_MOUSE PGCN_RAT
PGCV_CHICK PGCV_HUMAN PGCV_MOUSE PLK_BOVIN
PLK_CHICK PLK_HORSE PLK_HUMAN PLK_PIG
PLK_RAT Q92493 Q9Z1X7 TSG6_HUMAN
TSG6_RABIT
Sequence Titles
CD44_BOVIN  CD44 ANTIGEN PRECURSOR (PHAGOCYTIC GLYCOPROTEIN I) (PGP-1) (HUTCH-I) (EXTRACELLU 
CD44_CRIGR CD44 ANTIGEN PRECURSOR (PHAGOCYTIC GLYCOPROTEIN I) (PGP-1) (HUTCH-I) (EXTRACELLU
CD44_HORSE CD44 ANTIGEN PRECURSOR (PHAGOCYTIC GLYCOPROTEIN I) (PGP-1) (HUTCH-I) (EXTRACELLU
CD44_HUMAN CD44 ANTIGEN PRECURSOR (PHAGOCYTIC GLYCOPROTEIN I) (PGP-1) (HUTCH-I) (EXTRACELLU
CD44_MESAU CD44 ANTIGEN PRECURSOR (PHAGOCYTIC GLYCOPROTEIN I) (PGP-1) (HUTCH-I) (EXTRACELLU
CD44_MOUSE CD44 ANTIGEN PRECURSOR (PHAGOCYTIC GLYCOPROTEIN I) (PGP-1) (HUTCH-I) (EXTRACELLU
CD44_PAPHA CD44 ANTIGEN PRECURSOR (PHAGOCYTIC GLYCOPROTEIN I) (PGP-1) (HUTCH-I) (EXTRACELLU
CD44_RAT CD44 ANTIGEN PRECURSOR (PHAGOCYTIC GLYCOPROTEIN I) (PGP-1) (HUTCH-I) (EXTRACELLU
O08779 CD44 PROTEIN - RATTUS NORVEGICUS (RAT).
O08859 TUMOR NECROSIS FACTOR INDUCED PROTEIN 6 (TNF-STIMULATED GENE 6 PROTEIN) - MUS MU
O14594 NEUROCAN (PGCN_HUMAN) - HOMO SAPIENS (HUMAN).
O70509 GLYCOPROTEIN CD44S - RATTUS NORVEGICUS (RAT).
O77609 VERSICAN V0 SPLICE-VARIANT PRECURSOR - BOS TAURUS (BOVINE).
O77610 VERSICAN V1 SPLICE-VARIANT PRECURSOR - BOS TAURUS (BOVINE).
O77611 VERSICAN V2 SPLICE-VARIANT PRECURSOR - BOS TAURUS (BOVINE).
O77612 VERSICAN V3 SPLICE-VARIANT PRECURSOR - BOS TAURUS (BOVINE).
O88564 VERSICAN V3 ISOFORM PRECURSOR - RATTUS NORVEGICUS (RAT).
P79787 CHONDROITIN SULFATE PROTEOGLYCAN CORE PROTEIN - GALLUS GALLUS (CHICKEN).
PGCA_BOVIN AGGRECAN CORE PROTEIN PRECURSOR (CARTILAGE-SPECIFIC PROTEOGLYCAN CORE PROTEIN) (
PGCA_CHICK AGGRECAN CORE PROTEIN PRECURSOR (CARTILAGE-SPECIFIC PROTEOGLYCAN CORE PROTEIN) (
PGCA_HUMAN AGGRECAN CORE PROTEIN PRECURSOR (CARTILAGE-SPECIFIC PROTEOGLYCAN CORE PROTEIN) (
PGCA_MOUSE AGGRECAN CORE PROTEIN PRECURSOR (CARTILAGE-SPECIFIC PROTEOGLYCAN CORE PROTEIN) (
PGCA_RAT AGGRECAN CORE PROTEIN PRECURSOR (CARTILAGE-SPECIFIC PROTEOGLYCAN CORE PROTEIN) (
PGCB_BOVIN BREVICAN CORE PROTEIN PRECURSOR - BOS TAURUS (BOVINE).
PGCB_MOUSE BREVICAN CORE PROTEIN PRECURSOR - MUS MUSCULUS (MOUSE).
PGCB_RAT BREVICAN CORE PROTEIN PRECURSOR (BRAIN ENRICHED HYALURONAN BINDING PROTEIN) (BEH
PGCN_MOUSE NEUROCAN CORE PROTEIN PRECURSOR - MUS MUSCULUS (MOUSE).
PGCN_RAT NEUROCAN CORE PROTEIN PRECURSOR (245 KD EARLY POSTNATAL CORE GLYCOPROTEIN) [CONT
PGCV_CHICK VERSICAN CORE PROTEIN PRECURSOR (LARGE FIBROBLAST PROTEOGLYCAN) (CHONDROITIN SUL
PGCV_HUMAN VERSICAN CORE PROTEIN PRECURSOR (LARGE FIBROBLAST PROTEOGLYCAN) (CHONDROITIN SUL
PGCV_MOUSE VERSICAN CORE PROTEIN PRECURSOR (LARGE FIBROBLAST PROTEOGLYCAN) (CHONDROITIN SUL
PLK_BOVIN PROTEOGLYCAN LINK PROTEIN PRECURSOR (CARTILAGE LINK PROTEIN) (LP) - BOS TAURUS (
PLK_CHICK PROTEOGLYCAN LINK PROTEIN PRECURSOR (CARTILAGE LINK PROTEIN) (LP) - GALLUS GALLU
PLK_HORSE PROTEOGLYCAN LINK PROTEIN PRECURSOR (CARTILAGE LINK PROTEIN) (LP) - EQUUS CABALL
PLK_HUMAN PROTEOGLYCAN LINK PROTEIN PRECURSOR (CARTILAGE LINK PROTEIN) (LP) - HOMO SAPIENS
PLK_PIG PROTEOGLYCAN LINK PROTEIN PRECURSOR (CARTILAGE LINK PROTEIN) (LP) - SUS SCROFA (
PLK_RAT PROTEOGLYCAN LINK PROTEIN PRECURSOR (CARTILAGE LINK PROTEIN) (LP) - RATTUS NORVE
Q92493 CELL SURFACE GLYCOPROTEIN CD44 - HOMO SAPIENS (HUMAN).
Q9Z1X7 LINK PROTEIN - MUS MUSCULUS (MOUSE).
TSG6_HUMAN TUMOR NECROSIS FACTOR-INDUCIBLE PROTEIN TSG-6 PRECURSOR (HYALURONATE- BINDING PR
TSG6_RABIT TUMOR NECROSIS FACTOR-INDUCIBLE PROTEIN TSG-6 PRECURSOR (HYALURONATE- BINDING PR
Scan History
SPTR37_10f 2  100  NSINGLE    
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
RYTLNFTQAQQTC PGCV_CHICK 159 159 -
RYTLNFERAKQAC PGCA_CHICK 159 159 -
RYNLNFHEAQQAC PLK_CHICK 170 170 -
RYSISRTEAADLC CD44_PAPHA 41 41 -
KYKLTYAEAKAVC TSG6_HUMAN 46 46 -

Motif 2 width=14
Element Seqn Id St Int Rpt
AYEDGFEQCDAGWL PGCV_CHICK 187 15 -
AYEDGYEQCDAGWL PGCA_CHICK 187 15 -
AWRSGLDWCNAGWL PLK_CHICK 198 15 -
ALSIGFETCRYGFI CD44_PAPHA 69 15 -
ARKIGFHVCAAGWM TSG6_HUMAN 74 15 -

Motif 3 width=12
Element Seqn Id St Int Rpt
VRYPIRHPRIGC PGCV_CHICK 205 4 -
VRYPIHLPRERC PGCA_CHICK 205 4 -
VQYPITKPREPC PLK_CHICK 216 4 -
VVIPRIHPNSIC CD44_PAPHA 86 3 -
VGYPIVKPGPNC TSG6_HUMAN 92 4 -

Motif 4 width=10
Element Seqn Id St Int Rpt
YDVYCYVEHM PGCV_CHICK 238 21 -
YDVYCYAEQM PGCA_CHICK 238 21 -
YDVFCFTSNF PLK_CHICK 249 21 -
YDTYCFNASA CD44_PAPHA 114 16 -
WDAYCYNPHA TSG6_HUMAN 123 19 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
RYTLNFAAAQQAC PGCV_MOUSE 160 160 -
RYTLNFESAQQAC O88564 160 160 -
RYTLNFEMAQKAC O77609 161 161 -
RYTLNFEMAQKAC O77610 161 161 -
RYTLNFEMAQKAC O77611 161 161 -
RYTLNFEMAQKAC O77612 161 161 -
RYTLDFDRAQRAC PGCA_BOVIN 163 163 -
RYTLDFDRAQRAC PGCA_HUMAN 163 163 -
RYTLDFDRAQRAC PGCA_MOUSE 163 163 -
RYTLDFDRAQRAC PGCA_RAT 163 163 -
RYTLNFEAAQKAC PGCV_HUMAN 160 160 -
RYTLNFTQAQQTC PGCV_CHICK 159 159 -
RYTLNFERAKQAC P79787 159 159 -
RYTLNFERAKQAC PGCA_CHICK 159 159 -
RYALTFAEAQEAC O14594 170 170 -
RYALTFAEAQEAC PGCN_RAT 169 169 -
RYALTFAEAQEAC PGCN_MOUSE 169 169 -
RYAFSFAGAQEAC PGCB_BOVIN 167 167 -
RYAFSFAGAQEAC PGCB_MOUSE 166 166 -
RYAFSFAGAQEAC PGCB_RAT 166 166 -
RYNLNFHEAQQAC PLK_HORSE 169 169 -
RYNLNFHEAQQAC PLK_PIG 169 169 -
RYNLNFHEAQQAC PLK_HUMAN 169 169 -
RYNLNFHEAQQAC PLK_BOVIN 169 169 -
RYNLNFHEAQQAC PLK_CHICK 170 170 -
RYNLNFHEARQAC PLK_RAT 169 169 -
RYNLNFHEARQAC Q9Z1X7 170 170 -
RYSISRTEAADLC CD44_HUMAN 41 41 -
RYSISRTEAADLC CD44_PAPHA 41 41 -
RYSISRTEAADLC CD44_RAT 44 44 -
RYSISRTEAADLC O08779 44 44 -
RYSISRTEAADLC Q92493 41 41 -
RYSISRTEAADLC CD44_MOUSE 43 43 -
RYSISRTEAADLC O70509 44 44 -
RYSISRTEAADLC CD44_CRIGR 43 43 -
RYSISRTEAADLC CD44_MESAU 43 43 -
RYSISRTEAADLC CD44_HORSE 41 41 -
RYSISKTEAADLC CD44_BOVIN 41 41 -
RYKLTYAEAKAVC O08859 46 46 -
KYKLTYAEAKAVC TSG6_RABIT 46 46 -
KYKLTYAEAKAVC TSG6_HUMAN 46 46 -

Motif 2 width=14
Element Seqn Id St Int Rpt
AYEDGFEQCDAGWL PGCV_MOUSE 188 15 -
AYEDGFEQCDAGWL O88564 188 15 -
AYEDGFEQCDAGWL O77609 189 15 -
AYEDGFEQCDAGWL O77610 189 15 -
AYEDGFEQCDAGWL O77611 189 15 -
AYEDGFEQCDAGWL O77612 189 15 -
AYEDGFHQCDAGWL PGCA_BOVIN 191 15 -
AYEDGFHQCDAGWL PGCA_HUMAN 191 15 -
AYEDGFHQCDAGWL PGCA_MOUSE 191 15 -
AYEDGFHQCDAGWL PGCA_RAT 191 15 -
AYEDGFEQCDAGWL PGCV_HUMAN 188 15 -
AYEDGFEQCDAGWL PGCV_CHICK 187 15 -
AYEDGYEQCDAGWL P79787 187 15 -
AYEDGYEQCDAGWL PGCA_CHICK 187 15 -
AFEDGFDNCDAGWL O14594 198 15 -
AFEDGFDNCDAGWL PGCN_RAT 197 15 -
AFEDGFDNCDAGWL PGCN_MOUSE 197 15 -
AYLGGYEQCDAGWL PGCB_BOVIN 195 15 -
AYLGGYEQCDAGWL PGCB_MOUSE 194 15 -
AYLGGYEQCDAGWL PGCB_RAT 194 15 -
AWRGGLDWCNAGWL PLK_HORSE 197 15 -
AWRGGLDWCNAGWL PLK_PIG 197 15 -
AWRGGLDWCNAGWL PLK_HUMAN 197 15 -
AWRSGLDWCNAGWL PLK_BOVIN 197 15 -
AWRSGLDWCNAGWL PLK_CHICK 198 15 -
AWRGGLDWCNAGWL PLK_RAT 197 15 -
AWRGGLDWCNAGWL Q9Z1X7 198 15 -
ALSIGFETCRYGFI CD44_HUMAN 69 15 -
ALSIGFETCRYGFI CD44_PAPHA 69 15 -
ALRKGFETCRYGFI CD44_RAT 72 15 -
ALRKGFETCRYGFI O08779 72 15 -
ALSIGFETCRYGFI Q92493 69 15 -
ALSKGFETCRYGFI CD44_MOUSE 71 15 -
ALSKGFETCRYGFI O70509 72 15 -
ALSKGFETCRYGFI CD44_CRIGR 71 15 -
ALSKGFETCRYGFI CD44_MESAU 71 15 -
ALNIGFETCRIGFI CD44_HORSE 69 15 -
ARNIGFETCRYGFI CD44_BOVIN 69 15 -
ARKIGFHVCAAGWM O08859 74 15 -
ARKIGFHVCAAGWM TSG6_RABIT 74 15 -
ARKIGFHVCAAGWM TSG6_HUMAN 74 15 -

Motif 3 width=12
Element Seqn Id St Int Rpt
VRYPIRAPREGC PGCV_MOUSE 206 4 -
VRYPIRAPREGC O88564 206 4 -
VRYPIRVPREGC O77609 207 4 -
VRYPIRVPREGC O77610 207 4 -
VRYPIRVPREGC O77611 207 4 -
VRYPIRVPREGC O77612 207 4 -
VRYPIHTPREGC PGCA_BOVIN 209 4 -
VRYPIHTPREGC PGCA_HUMAN 209 4 -
VRYPIHTPREGC PGCA_MOUSE 209 4 -
VRYPIHTPREGC PGCA_RAT 209 4 -
VRYPIRAPRVGC PGCV_HUMAN 206 4 -
VRYPIRHPRIGC PGCV_CHICK 205 4 -
VRYPIHLPRERC P79787 205 4 -
VRYPIHLPRERC PGCA_CHICK 205 4 -
VRYPITQSRPGC O14594 216 4 -
VRYPITQSRPGC PGCN_RAT 215 4 -
VRYPITQSRPGC PGCN_MOUSE 215 4 -
VRYPIQTPREAC PGCB_BOVIN 213 4 -
VRYPIQNPREAC PGCB_MOUSE 212 4 -
VRYPIQNPREAC PGCB_RAT 212 4 -
VQYPITKPREPC PLK_HORSE 215 4 -
VQYPITKPREPC PLK_PIG 215 4 -
VQYPITKPREPC PLK_HUMAN 215 4 -
VQYPITKPREPC PLK_BOVIN 215 4 -
VQYPITKPREPC PLK_CHICK 216 4 -
VQYPITKPREPC PLK_RAT 215 4 -
VQYPITKPREPC Q9Z1X7 216 4 -
VVIPRIHPNSIC CD44_HUMAN 86 3 -
VVIPRIHPNSIC CD44_PAPHA 86 3 -
VVIPRIHPNAIC CD44_RAT 89 3 -
VVIPRIHPNAIC O08779 89 3 -
VVIPRIHPNSIC Q92493 86 3 -
VVIPRIHPNAIC CD44_MOUSE 88 3 -
VVIPRIHPNAIC O70509 89 3 -
VVIPRIQPNAIC CD44_CRIGR 88 3 -
VVIPRIQPNAIC CD44_MESAU 88 3 -
VVIPPIHPNSIC CD44_HORSE 86 3 -
VVIPRIHPNSIC CD44_BOVIN 86 3 -
VGYPIVKPGPNC O08859 92 4 -
VGYPIVKPGSNC TSG6_RABIT 92 4 -
VGYPIVKPGPNC TSG6_HUMAN 92 4 -

Motif 4 width=10
Element Seqn Id St Int Rpt
YDVYCYVDHL PGCV_MOUSE 239 21 -
YDVYCYVDHL O88564 239 21 -
YDVYCYVDHL O77609 240 21 -
YDVYCYVDHL O77610 240 21 -
YDVYCYVDHL O77611 240 21 -
YDVYCYVDHL O77612 240 21 -
YDVYCFAEEM PGCA_BOVIN 242 21 -
YDVYCFAEEM PGCA_HUMAN 242 21 -
YDVYCFAEEM PGCA_MOUSE 242 21 -
YDVYCFAEEM PGCA_RAT 242 21 -
YDVYCYVDHL PGCV_HUMAN 239 21 -
YDVYCYVEHM PGCV_CHICK 238 21 -
YDVYCYAEQM P79787 238 21 -
YDVYCYAEQM PGCA_CHICK 238 21 -
YDVYCFAREL O14594 249 21 -
YDVYCFAREL PGCN_RAT 248 21 -
YDVYCFAREL PGCN_MOUSE 248 21 -
YDVYCYAEEL PGCB_BOVIN 246 21 -
YDVYCYAEDL PGCB_MOUSE 245 21 -
YDVYCYAEDL PGCB_RAT 245 21 -
YDVFCFTSNF PLK_HORSE 248 21 -
YDVFCFTSNF PLK_PIG 248 21 -
YDVFCFTSNF PLK_HUMAN 248 21 -
YDVFCFTSNF PLK_BOVIN 248 21 -
YDVFCFTSNF PLK_CHICK 249 21 -
YDVFCFTSNF PLK_RAT 248 21 -
YDVFCFTSNF Q9Z1X7 249 21 -
YDTYCFNASA CD44_HUMAN 114 16 -
YDTYCFNASA CD44_PAPHA 114 16 -
YDTYCFNASA CD44_RAT 118 17 -
YDTYCFNASA O08779 118 17 -
YDTYCFNASA Q92493 114 16 -
YDTYCFNASA CD44_MOUSE 117 17 -
YDTYCFNASA O70509 118 17 -
YDTYCFNASA CD44_CRIGR 116 16 -
YDTYCFNASA CD44_MESAU 116 16 -
YDTYCFNASA CD44_HORSE 114 16 -
YDTICFNASA CD44_BOVIN 114 16 -
WDAYCYNPHA O08859 123 19 -
WDAYCYNPHA TSG6_RABIT 123 19 -
WDAYCYNPHA TSG6_HUMAN 123 19 -