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PR00864

Identifier
PREPILNPTASE  [View Relations]  [View Alignment]  
Accession
PR00864
No. of Motifs
4
Creation Date
26-APR-1998  (UPDATE 28-JUL-1999)
Title
Type IV prepilin cysteine protease (C20) family signature
Database References

INTERPRO; IPR000045
Literature References
1. RAWLINGS, N.D. AND BARRETT, A.J.
Families of cysteine peptidases.
METHODS ENZYMOL. 244 461-486 (1994).
 
2. RAWLINGS, N.D. AND BARRETT, A.J.
Evolutionary families of peptidases.
BIOCHEM.J. 290 205-218 (1993).
 
3. BAIROCH, A. AND RAWLINGS, N.
Classification of peptidase families and index of peptidase entries in
SWISS-PROT.
http://expasy.hcuge.ch/cgi-bin/lists?peptidas.txt

Documentation
Cysteine protease activity is dependent on an active dyad of cysteine and
histidine, the order and spacing of these residues varying in the 20 or so
known families. Cysteine proteases have been grouped into two clans (CA and
CB). Families C1, C2 and C10 are loosely termed papain-like and belong 
to clan CA; five cysteine proteases belong to clan CB; other families have
not been assigned to clans. Nearly half of all cysteine proteases are found 
exclusively in viruses. The order of catalytic cysteine and histidine 
residues within the primary structure differs between the families and is 
an indication of convergent evolution [1-3].
 
Bacteria produce a number of protein precursors that undergo post-
translational methylation and proteolysis prior to secretion as active
proteins. Type IV prepilin leader peptidases, which belong to the C20 family
of cysteine proteases, are enzymes that mediate this type of post-
translational modification. Type IV pilin is a protein found on the surface
of Pseudomonas aeruginosa, Neisseria gonorrhoeae and other Gram-negative
pathogens. Pilin subunits attach the infecting organism to the surface of 
host epithelial cells. They are synthesised as prepilin subunits, which 
differ from mature pilin by virtue of containing a 6-8 residue leader
peptide consisting of charged amino acids. Mature type IV pilins also
contain a methylated N-terminal phenylalanine residue. 
 
Prepilin leader peptidases are found on the cytosolic membrane surface,
where they have dual activity, involving cleavage of glycine-phenylalanine
bonds and methylation of the newly-revealed N-terminal phenylalanine. The
consensus sequence for the site of proteolytic cleavage is -G+F-T-L/I-, in
which the Gly P1 residue is essential [1]. The peptidases are suseptible to 
thiol blocking reagents. Site directed mutagenesis has indicated four highly
conserved cysteine residues that affect both the protease and methylase 
activity.
 
PREPILNPTASE is a 4-element fingerprint that provides a signature for the 
type IV leaderpeptidase (C20) family of cysteine proteases. The fingerprint
was derived from an initial alignment of 13 sequences: the motifs were drawn
from conserved regions spanning the central portion of the alignment. Two
iterations on OWL30.1 were required to reach convergence, at which point a
true set comprising 19 sequences was found. 
 
An update on SPTR37_9f identified a true set of 23 sequences, and 5
partial matches.
Summary Information
  23 codes involving  4 elements
3 codes involving 3 elements
2 codes involving 2 elements
Composite Feature Index
423232323
33132
22020
1234
True Positives
LEP3_AERHY    LEP3_ECOLI    LEP3_ERWCA    LEP3_ERWCH    
LEP3_KLEPN LEP3_NEIGO LEP3_PSEAE LEP3_PSEPU
LEP3_VIBCH O30387 O32576 O53004
O54483 O68839 O68927 O68964
P72640 Q46525 Q46836 Q53404
Q56668 Q56740 Q56763
True Positive Partials
Codes involving 3 elements
LEP3_BACSU O68433 O68932
Codes involving 2 elements
P94648 Q57382
Sequence Titles
LEP3_AERHY  TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3.4.99.-) - AEROMONAS HYDROPHILA. 
LEP3_ECOLI TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3.4.99.-) - ESCHERICHIA COLI.
LEP3_ERWCA TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3.4.99.-) (PECTIC ENZYMES SECRETION PROTEIN OUTO) - ERWINIA CAROTOVORA.
LEP3_ERWCH TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3.4.99.-) (PECTIC ENZYMES SECRETION PROTEIN OUTO) - ERWINIA CHRYSANTHEMI.
LEP3_KLEPN TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3.4.99.-) (PULLULANASE SECRETION PROTEIN PULO) - KLEBSIELLA PNEUMONIAE.
LEP3_NEIGO TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3.4.99.-) - NEISSERIA GONORRHOEAE.
LEP3_PSEAE TYPE 4 PREPILIN PEPTIDASE (EC 3.4.99.-) (PROTEIN SECRETION PROTEIN XCPA) (PILD PROTEIN) - PSEUDOMONAS AERUGINOSA.
LEP3_PSEPU TYPE 4 PREPILIN PEPTIDASE (EC 3.4.99.-) (PROTEIN SECRETION PROTEIN XCPA) (PILD PROTEIN) - PSEUDOMONAS PUTIDA.
LEP3_VIBCH TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3.4.99.-) - VIBRIO CHOLERAE.
O30387 PILD - MYXOCOCCUS XANTHUS.
O32576 ETPN PROTEIN - ESCHERICHIA COLI.
O53004 ORF2 PROTEIN - ESCHERICHIA COLI.
O54483 PILD - AEROMONAS SALMONICIDA.
O68839 TYPE 4 PREPILIN PEPTIDASE VCPD - VIBRIO CHOLERAE.
O68927 LEADER PEPTIDASE HOPD - SALMONELLA TYPHIMURIUM.
O68964 TYPE IV PREPILIN PEPTIDASE TAPD - AEROMONAS SALMONICIDA.
P72640 TYPE 4 PREPILIN PEPTIDASE - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
Q46525 FIMP - BACTEROIDES NODOSUS (DICHELOBACTER NODOSUS).
Q46836 ORF_F310 - ESCHERICHIA COLI.
Q53404 TYPE IV PREPILIN PEPTIDASE - NEISSERIA GONORRHOEAE.
Q56668 TOXIN CO-REGULATED PILUS - VIBRIO CHOLERAE.
Q56740 VVPD - VIBRIO VULNIFICUS.
Q56763 XPSO - XANTHOMONAS CAMPESTRIS.

LEP3_BACSU TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3.4.99.-) (LATE COMPETENCE PROTEIN COMC) - BACILLUS SUBTILIS.
O68433 TYPE IV PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE PILD - LEGIONELLA PNEUMOPHILA.
O68932 LEADER PEPTIDASE HOPD - ESCHERICHIA COLI.

P94648 PREPILIN PEPTIDASE HOMOLOG - CHLOROBIUM LIMICOLA.
Q57382 BFPP - ESCHERICHIA COLI.
Scan History
OWL30_0    2  550  NSINGLE    
SPTR37_9f 2 100 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
LAAIDARTQLLPDVMTLP LEP3_ERWCH 145 145 -
LAAIDAQTQLLPDGLTLP LEP3_KLEPN 133 133 -
MSLIDADHQLLPDVLVLP LEP3_PSEAE 145 145 -
LTFIDLDKMLLPDQLTLP LEP3_AERHY 147 147 -
LTLIDWDTMTLPNSLTKP S74490 117 117 -
LAFIDLDHWILPLSMTVP AF0036323 122 122 -
LAVIDCHTALLPDVLTLP ECPO15711 107 107 -
VAVTDIHFMLIPNRILIF LEP3_BACSU 109 109 -
LFVIDFKSMLLPNLLTYP LEP3_VIBCH 121 121 -
LTFIDADTQYLPDSMTLP LEP3_NEIGO 143 143 -
LTVIDIKTLLLPDELTLS LEP3_ERWCA 144 144 -
LSVIDFRTQLLPDKLTLP LEP3_ECOLI 90 90 -
LSLIDHDQQLLPDAIVLP LEP3_PSEPU 144 144 -

Motif 2 width=11
Element Seqn Id St Int Rpt
KVFQREALGAG AF0036323 179 39 -
FATGREGLGYG ECPO15711 164 39 -
LLLGREGMGDG S74490 180 45 -
AAITHGGVGGG LEP3_BACSU 161 34 -
LLTGKEGMGYG LEP3_AERHY 204 39 -
LVTGKEGMGYG LEP3_PSEAE 202 39 -
LLSGKEALGYG LEP3_KLEPN 190 39 -
LLSGREALGHG LEP3_ERWCH 202 39 -
LVTGKEGMGYG LEP3_PSEPU 201 39 -
LVCHKEGLGYG LEP3_ECOLI 147 39 -
YATGKEALGYG LEP3_ERWCA 201 39 -
LLTGKTGMGNG LEP3_NEIGO 200 39 -
LFKRIDVMGGG LEP3_VIBCH 178 39 -

Motif 3 width=12
Element Seqn Id St Int Rpt
DFKLLAAAGAWC LEP3_ECOLI 158 0 -
DFKLLAALGAWL LEP3_ERWCA 212 0 -
DFKLIAALGAWL LEP3_NEIGO 211 0 -
DIKLYTAIGTLI LEP3_VIBCH 189 0 -
DFKLLAALGAWL LEP3_AERHY 215 0 -
DFKLLAMLGAWG LEP3_PSEAE 213 0 -
DFKLLAALGAWL LEP3_KLEPN 201 0 -
DFKLLAALGAWL LEP3_ERWCH 213 0 -
DIKLFAVIGFVL LEP3_BACSU 172 0 -
DKYLVAMLGAFL AF0036323 190 0 -
DPKLASMVGAWL S74490 191 0 -
DFKLAAALGAWM ECPO15711 175 0 -
DFKLLALLGAWG LEP3_PSEPU 212 0 -

Motif 4 width=16
Element Seqn Id St Int Rpt
GWQALPIVLLLSSLVG LEP3_AERHY 227 0 -
GWQALPQTLLLASPAA LEP3_KLEPN 213 0 -
GWQALPNLVLIASLTG LEP3_ERWCH 225 0 -
GWQVLPLTLLLSSVLG LEP3_PSEPU 224 0 -
GWQTLPMILLIASLGG LEP3_ECOLI 170 0 -
GWQALPNLVLVAALSG LEP3_ERWCA 224 0 -
GISALPVLIFVSSLIG LEP3_NEIGO 223 0 -
GVEFVPYLFLLSSIIA LEP3_VIBCH 201 0 -
GVKMLAAAFFFSVLIG LEP3_BACSU 184 0 -
TWRALLGVLLFASMQG AF0036323 202 0 -
GWPSLLLTTFIACFIG S74490 203 0 -
GWQALPSILLFASVSG ECPO15711 187 0 -
GWQILPLTILLSSLVG LEP3_PSEAE 225 0 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
LTFIDLDKMLLPDQLTLP LEP3_AERHY 147 147 -
LTFIDLDKMLLPDQLTLP O68964 148 148 -
ATFIDLDTMLLPDQLTLP Q56740 143 143 -
ATFIDFDTLLLPDQLTLP O68839 143 143 -
LTFIDLDKMLLXDQLNLX O54483 148 148 -
MSLIDADHQLLPDVLVLP LEP3_PSEAE 145 145 -
LAAIDAQTQLLPDGLTLP LEP3_KLEPN 133 133 -
LAVIDCHTALLPDVLTLP O32576 107 107 -
LAVIDCHTALLPDVLTLP O53004 107 107 -
LAAIDARTQLLPDVMTLP LEP3_ERWCH 145 145 -
LSLIDHDQQLLPDAIVLP LEP3_PSEPU 144 144 -
LSVIDFRTQLLPDKLTLP LEP3_ECOLI 90 90 -
LTVIDIKTLLLPDELTLS LEP3_ERWCA 144 144 -
LTFIDADTQYLPDSMTLP LEP3_NEIGO 143 143 -
LTFIDEDTQYLPDSMTLP Q53404 143 143 -
MSGIDLRHKLLPDQLTLP Q56763 142 142 -
LCFIDAEHQLLPDRLTLP Q46525 147 147 -
LTLIDWDTMTLPNSLTKP P72640 117 117 -
LGIYDARTGLLPDRFTCP O68927 18 18 -
ASVIDLDHQWLPDVFTQG Q46836 180 180 -
LAFIDLDHWILPLSMTVP O30387 122 122 -
LFVIDFKSMLLPNLLTYP LEP3_VIBCH 121 121 -
LFVIDFKSMLLPNLLTYP Q56668 121 121 -

Motif 2 width=11
Element Seqn Id St Int Rpt
LLTGKEGMGYG LEP3_AERHY 204 39 -
LLTGKEGMGYG O68964 205 39 -
LLTGKEGMGYG Q56740 201 40 -
LLTGKEGMGYG O68839 201 40 -
LLTGKEGMGYG O54483 205 39 -
LVTGKEGMGYG LEP3_PSEAE 202 39 -
LLSGKEALGYG LEP3_KLEPN 190 39 -
FATGREGLGYG O32576 164 39 -
FATGREGLGYG O53004 164 39 -
LLSGREALGHG LEP3_ERWCH 202 39 -
LVTGKEGMGYG LEP3_PSEPU 201 39 -
LVCHKEGLGYG LEP3_ECOLI 147 39 -
YATGKEALGYG LEP3_ERWCA 201 39 -
LLTGKTGMGNG LEP3_NEIGO 200 39 -
LLTGKTGMGNG Q53404 200 39 -
QLTGKEGMGHG Q56763 199 39 -
LITGREGMGYG Q46525 204 39 -
LLLGREGMGDG P72640 180 45 -
LRYQKEGLGYG O68927 75 39 -
IVLRKEALGMG Q46836 238 40 -
KVFQREALGAG O30387 179 39 -
LFKRIDVMGGG LEP3_VIBCH 178 39 -
LFKRIDVMGGG Q56668 178 39 -

Motif 3 width=12
Element Seqn Id St Int Rpt
DFKLLAALGAWL LEP3_AERHY 215 0 -
DFKLLAALGAWL O68964 216 0 -
DFKLLAALGAWL Q56740 212 0 -
DFKLLAALGAWL O68839 212 0 -
DFKLLAALGAWL O54483 216 0 -
DFKLLAMLGAWG LEP3_PSEAE 213 0 -
DFKLLAALGAWL LEP3_KLEPN 201 0 -
DFKLAAALGAWM O32576 175 0 -
DFKLAAALGAWM O53004 175 0 -
DFKLLAALGAWL LEP3_ERWCH 213 0 -
DFKLLALLGAWG LEP3_PSEPU 212 0 -
DFKLLAAAGAWC LEP3_ECOLI 158 0 -
DFKLLAALGAWL LEP3_ERWCA 212 0 -
DFKLIAALGAWL LEP3_NEIGO 211 0 -
DFKLIAALGAWL Q53404 211 0 -
DFKLLAALGAWC Q56763 210 0 -
DFKLLACLCAWQ Q46525 215 0 -
DPKLASMVGAWL P72640 191 0 -
DVKYLAALGAWH O68927 86 0 -
DVLLFAALGGWV Q46836 249 0 -
DKYLVAMLGAFL O30387 190 0 -
DIKLYTAIGTLI LEP3_VIBCH 189 0 -
DIKLYTAIGTLI Q56668 189 0 -

Motif 4 width=16
Element Seqn Id St Int Rpt
GWQALPIVLLLSSLVG LEP3_AERHY 227 0 -
GWQALPIVLLLSSLVG O68964 228 0 -
GWQYLPMIILLSSVVG Q56740 224 0 -
GWQQLPVIVLLSSVVG O68839 224 0 -
GWQALPIVLLLSSLVG O54483 228 0 -
GWQILPLTILLSSLVG LEP3_PSEAE 225 0 -
GWQALPQTLLLASPAA LEP3_KLEPN 213 0 -
GWQALPSILLFASVSG O32576 187 0 -
GWQALPSILLFASVSG O53004 187 0 -
GWQALPNLVLIASLTG LEP3_ERWCH 225 0 -
GWQVLPLTLLLSSVLG LEP3_PSEPU 224 0 -
GWQTLPMILLIASLGG LEP3_ECOLI 170 0 -
GWQALPNLVLVAALSG LEP3_ERWCA 224 0 -
GISALPVLIFVSSLIG LEP3_NEIGO 223 0 -
GISALPVLIFVSSLIG Q53404 223 0 -
GLKGILPIILISSLVG Q56763 222 0 -
GAWMLPIILFSAAILG Q46525 227 0 -
GWPSLLLTTFIACFIG P72640 203 0 -
CWETLPLLVFLAAMLA O68927 98 0 -
GALSLPNVALIASCCG Q46836 261 0 -
TWRALLGVLLFASMQG O30387 202 0 -
GVEFVPYLFLLSSIIA LEP3_VIBCH 201 0 -
GVEFVPYLFLLSSIIA Q56668 201 0 -