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PR00727

Identifier
LEADERPTASE  [View Relations]  [View Alignment]  
Accession
PR00727
No. of Motifs
3
Creation Date
10-MAY-1997  (UPDATE 27-JUN-1999)
Title
Bacterial leader peptidase 1 (S26A) family signature
Database References

PROSITE; PS00501 SPASE_I_1; PS00760 SPASE_I_2; PS00761 SPASE_I_3

BLOCKS; BL00501
PFAM; PF00461 Peptidase_S26
INTERPRO; IPR000223
Literature References
1. RAWLINGS, N.D. AND BARRETT, A.J.
Families of serine peptidases.
METHODS ENZYMOL. 244 19-61 (1994).
 
2. RAWLINGS, N.D AND BARRETT, A.J.
Evolutionary families of peptidases.
BIOCHEM.J. 290 205-218 (1993).

Documentation
Proteolytic enzymes that exploit serine in their catalytic activity are
ubiquitous, being found in viruses, bacteria and eukaryotes [1]. They 
include a wide range of peptidase activity, including exopeptidase, endo-
peptidase, oligopeptidase and omega-peptidase activity. Over 20 families
(denoted S1-S26) of serine protease have been identified, these being
grouped into 6 clans (SA, SB, SC, SE, SF and SG) on the basis of structural
similarity and other functional evidence [1]. Structures are known for four
of the clans (SA, SB, SC and SE): these appear to be totally unrelated,
suggesting at least four evolutionary origins of serine peptidases and
possibly many more [1].
 
Notwithstanding their different evolutionary origins, there are similarities
in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin
and carboxypeptidase C clans have a catalytic triad of serine, aspartate and 
histidine in common: serine acts as a nucleophile, aspartate as an
electrophile, and histidine as a base [1]. The geometric orientations of
the catalytic residues are similar between families, despite different 
protein folds [1]. The linear arrangements of the catalytic residues
commonly reflect clan relationships. For example the catalytic triad in 
the chymotrypsin clan (SA) is ordered HDS, but is ordered DHS in the
subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [1,2].
 
At least 3 eubacterial leader peptidases are known: murein prelipoprotein 
peptidase, which cleaves the leader peptide from a component of the
bacterial outer membrane; type IV prepilin leader peptidase; and the serine-
dependent leader peptidase 1, which has the more general role of cleaving
the leader peptide from a variety of secreted proteins and proteins directed
to the periplasm and periplasmic membrane [1]. Leader peptidase 1 is
similar to the eukaryotic signal peptidase, although the bacterial protein
is monomeric, while the eukaryotic protein is multimeric [1].
 
Mitochondria contain a similar two-subunit serine protease that removes
leader peptides from nuclear- and mitochondrially-encoded proteins, which
localise in the inner mitochondrial space [1]. The catalytic residues of a
number of these peptides have been identified as a serine/lysine dyad [1].
 
LEADERPTASE is a 3-element fingerprint that provides a signature for the 
bacterial leader peptidase 1 (S26A) family. The fingerprint was derived from
an initial alignment of 6 sequences: the motifs were drawn from conserved
regions spanning virtually the full alignment length - motif 1 includes the
region encoded by PROSITE pattern SPASE_I_1 (PS00501), which contains the
catalytic serine; motif 2 includes the region encoded by PROSITE pattern
SPASE_I_2 (PS00760), which contains the active lysine; and motif 3 includes
the region encoded by PROSITE pattern SPASE_I_3 (PS00761), a conserved
C-terminal region of unknown function. Two iterations on OWL29.3 were
required to reach convergence, at which point a true set comprising 23
sequences was identified. 
 
An update on SPTR37_9f identified a true set of 42 sequences, and 2
partial matches.
Summary Information
  42 codes involving  3 elements
2 codes involving 2 elements
Composite Feature Index
3424242
2202
123
True Positives
IMP1_YEAST    IMP2_YEAST    LEPA_BACAM    LEPC_BACCL    
LEPH_STAAU LEPP_BACNA LEPQ_BACNA LEPS_BACSU
LEPT_BACSU LEPU_BACSU LEP_BACAM LEP_BACLI
LEP_ECOLI LEP_HAEIN LEP_MYCTU LEP_PHOLA
LEP_PSEFL LEP_SALTY LEP_STAAU LEP_STRPN
O04348 O07560 O25300 O33021
O51061 O54237 O67088 O69160
O69884 O69885 O69886 O69887
O74800 O83215 O83896 O84023
O86869 O86870 P72660 P73157
Q45225 Q52697
True Positive Partials
Codes involving 2 elements
O51062 O51278
Sequence Titles
IMP1_YEAST  MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 1 (EC 3.4.99.-) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). 
IMP2_YEAST MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2 (EC 3.4.99.-) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
LEPA_BACAM SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - BACILLUS AMYLOLIQUEFACIENS.
LEPC_BACCL SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - BACILLUS CALDOLYTICUS.
LEPH_STAAU INACTIVE SIGNAL PEPTIDASE IA - STAPHYLOCOCCUS AUREUS.
LEPP_BACNA SIGNAL PEPTIDASE I P (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - BACILLUS SUBTILIS VAR. NATTO.
LEPQ_BACNA SIGNAL PEPTIDASE I P (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - BACILLUS SUBTILIS VAR. NATTO.
LEPS_BACSU SIGNAL PEPTIDASE I S (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - BACILLUS SUBTILIS.
LEPT_BACSU SIGNAL PEPTIDASE I T (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - BACILLUS SUBTILIS.
LEPU_BACSU SIGNAL PEPTIDASE I U (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - BACILLUS SUBTILIS.
LEP_BACAM SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - BACILLUS AMYLOLIQUEFACIENS.
LEP_BACLI SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - BACILLUS LICHENIFORMIS.
LEP_ECOLI SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - ESCHERICHIA COLI.
LEP_HAEIN SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - HAEMOPHILUS INFLUENZAE.
LEP_MYCTU PROBABLE SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - MYCOBACTERIUM TUBERCULOSIS.
LEP_PHOLA SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - PHORMIDIUM LAMINOSUM.
LEP_PSEFL SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - PSEUDOMONAS FLUORESCENS.
LEP_SALTY SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - SALMONELLA TYPHIMURIUM.
LEP_STAAU SIGNAL PEPTIDASE IB (EC 3.4.21.89) (SPASE IB) (LEADER PEPTIDASE IB) - STAPHYLOCOCCUS AUREUS.
LEP_STRPN SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - STREPTOCOCCUS PNEUMONIAE.
O04348 CHLOROPLAST THYLAKOIDAL PROCESSING PEPTIDASE (LEADER PEPTIDASE I ISOLOG) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O07560 HYPOTHETICAL 19.0 KD PROTEIN - BACILLUS SUBTILIS.
O25300 SIGNAL PEPTIDASE I (LEPB) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
O33021 SIGNAL PEPTIDASE I - MYCOBACTERIUM LEPRAE.
O51061 SIGNAL PEPTIDASE I (LEPB-1) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O54237 SIGNAL PEPTIDASE I - STREPTOMYCES LIVIDANS.
O67088 TYPE-I SIGNAL PEPTIDASE - AQUIFEX AEOLICUS.
O69160 PROKARYOTIC TYPE I SIGNAL PEPTIDASE SIPF - BRADYRHIZOBIUM JAPONICUM.
O69884 PUTATIVE SIGNAL PEPTIDASE I - STREPTOMYCES COELICOLOR, AND STREPTOMYCES LIVIDANS.
O69885 PUTATIVE SIGNAL PEPTIDASE I - STREPTOMYCES COELICOLOR.
O69886 PUTATIVE SIGNAL PEPTIDASE I - STREPTOMYCES COELICOLOR, AND STREPTOMYCES LIVIDANS.
O69887 PUTATIVE SIGNAL PEPTIDASE I - STREPTOMYCES COELICOLOR.
O74800 PUTATIVE MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2 - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
O83215 SIGNAL PEPTIDASE I (SIP) - TREPONEMA PALLIDUM.
O83896 SIGNAL PEPTIDASE I, PUTATIVE - TREPONEMA PALLIDUM.
O84023 SIGNAL PEPTIDASE I - CHLAMYDIA TRACHOMATIS.
O86869 SIGNAL PEPTIDASE I - STREPTOMYCES LIVIDANS.
O86870 SIGNAL PEPTIDASE I - STREPTOMYCES LIVIDANS.
P72660 LEADER PEPTIDASE I - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
P73157 LEADER PEPTIDASE I - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
Q45225 SIPS - BRADYRHIZOBIUM JAPONICUM.
Q52697 LEADER PEPTIDASE - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).

O51062 SIGNAL PEPTIDASE I (LEPB-2) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O51278 SIGNAL PEPTIDASE I (LEPB-3) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
Scan History
OWL29_3    2  100  NSINGLE    
SPTR37_9f 2 100 NSINGLE
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
FLYEPFQIPSGSMMPTL LEP_SALTY 80 80 -
FVARPYLIPSESMEPTL LEP_MYCTU 85 85 -
FLFEPYVVEGKSMDPTL LEPP_BACSU 33 33 -
FLFEPYLVEGTSMDPTL LEP_BACLI 33 33 -
FLVEPFQIPSGSMKPTL LEP_PSEFL 79 79 -
FLFAPYVVDGESMEPTL LEPA_BACAM 34 34 -

Motif 2 width=13
Element Seqn Id St Int Rpt
YIKRVVGLPGDVV LEP_PSEFL 143 47 -
YVKRLIGLPGDTV LEPP_BACSU 84 34 -
YVKRLIGLPGDTV LEP_BACLI 84 34 -
YVKRIIGLPGDTV LEPA_BACAM 83 32 -
YIKRAVGLPGDKI LEP_SALTY 144 47 -
LVKRVIAVGGQTV LEP_MYCTU 172 70 -

Motif 3 width=20
Element Seqn Id St Int Rpt
VPPGRVWVMGDNRTHSADSR LEP_MYCTU 228 43 -
VPEGKYFVMGDNRQRSMDSR LEP_BACLI 138 41 -
VPAGHYFMMGDNRDNSNDSR LEP_PSEFL 216 60 -
VPKDKYFVMGDNRQESMDSR LEPP_BACSU 138 41 -
VPDDKYFVMGDNRRNSMDSR LEPA_BACAM 137 41 -
VPPGQYFMMGDNRDNSADSR LEP_SALTY 264 107 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
FLFEPYLVEGTSMDPTL LEP_BACLI 33 33 -
FLVEPFQIPSGSMKPTL LEP_PSEFL 79 79 -
FLFAPYVVDGESMEPTL LEPA_BACAM 34 34 -
FLFEPYVVEGKSMDPTL LEPP_BACNA 33 33 -
FIYEPFQIPSGSMMPTL LEP_ECOLI 80 80 -
FLFQPFNIPSGSMKATL O69160 33 33 -
FLFEPYLVEGSSMYPTL LEP_BACAM 40 40 -
FLFEPYLVEGSSMYPTL LEPT_BACSU 40 40 -
FLFEPYIVQGESMKPTL LEPQ_BACNA 32 32 -
FIFAPYVVDGDSMYPTL LEPS_BACSU 32 32 -
FLYEPFQIPSGSMMPTL LEP_SALTY 80 80 -
ALAEPFYVPSGSMEPTL Q45225 38 38 -
FLFEPFQIPSGSMESTL LEP_HAEIN 104 104 -
FVAEPRYIPSDSMLPTL P72660 33 33 -
FLVQAFSIPSSSMENTL O69886 103 103 -
FLVQAFSIPSSSMENTL O54237 58 58 -
FVAEARYIPSSSMEPTL P73157 41 41 -
FVARPYLIPSESMEPTL LEP_MYCTU 85 85 -
FVARPYLIPSESMEPTL O33021 73 73 -
YIAQAYTIPSASMEPTL O67088 21 21 -
FIVTPYTIKGESMDPTL LEP_STAAU 25 25 -
FVFSNYVVEGKSMMPTL LEPC_BACCL 27 27 -
FVAEARYIPSESMLPTL LEP_PHOLA 48 48 -
VFYKPFLIEGSSMAPTL LEPU_BACSU 35 35 -
LFFQPFWIPSGSMKDTL Q52697 29 29 -
FLVQAFVIPSGSMEQTI O69885 74 74 -
FLVQAFVIPSGSMEQTI O86869 74 74 -
FVLQPFQIPSGSMERGL O69884 66 66 -
AVFIDYKVEGVSMNPTF O07560 23 23 -
FWFELYEVPTGSMRPTI O84023 102 102 -
ALAEPKSIPSTSMYPTL O04348 173 173 -
FFWSNVRVEGHSMDPTL LEP_STRPN 27 27 -
VVYRPYTVPTSSMTPTI O69887 50 50 -
VVYRPYTVPTSSMTPTI O86870 50 50 -
FAFQLYVIPSESMVPSF O83896 76 76 -
YAYEFTETRGESMLPTL IMP1_YEAST 28 28 -
FIAQAFIIPSRSMVGTL O25300 27 27 -
HVVAAYRIQADSMQPTL O83215 40 40 -
YLFQVQMTSGPSMMPTL O74800 24 24 -
NVVHIAQVKGTSMQPTL IMP2_YEAST 30 30 -
FVIVGHVIPNNDMSPTL LEPH_STAAU 24 24 -
FVLQIFMIKSNEMLPTI O51061 37 37 -

Motif 2 width=13
Element Seqn Id St Int Rpt
YVKRLIGLPGDTV LEP_BACLI 84 34 -
YIKRVVGLPGDVV LEP_PSEFL 143 47 -
YVKRIIGLPGDTV LEPA_BACAM 83 32 -
YVKRLIGLPGDTV LEPP_BACNA 84 34 -
YIKRAVGLPGDKV LEP_ECOLI 144 47 -
YIKRVIGLPGDRV O69160 103 53 -
YVKRLIGKPGETV LEP_BACAM 91 34 -
YVKRLIGKPGETV LEPT_BACSU 91 34 -
YVKRLIGLPGDTI LEPQ_BACNA 83 34 -
YVKRIIGLPGDTV LEPS_BACSU 81 32 -
YIKRAVGLPGDKI LEP_SALTY 144 47 -
WVKRVVGLPGDRI Q45225 109 54 -
YIKRIVGKGGDRV LEP_HAEIN 194 73 -
FIKRVIALPGQTV P72660 92 42 -
LIKRVIGVAGDTV O69886 182 62 -
LIKRVIGVAGDTV O54237 137 62 -
FIKRIIGLPGDEV P73157 98 40 -
LVKRVIAVGGQTV LEP_MYCTU 172 70 -
LVKRVIAVGGQTV O33021 160 70 -
FIKRIIARGGDTV O67088 73 35 -
YVKRVIGVPGDKV LEP_STAAU 75 33 -
YVKRVIGLPGDRI LEPC_BACCL 77 33 -
FIKRVIGLPGETV LEP_PHOLA 107 42 -
FVKRLIGLPGDSI LEPU_BACSU 86 34 -
FIKRLIGLPGDRI Q52697 103 57 -
LIKRVVGVGGDHV O69885 159 68 -
LIKRVVGVGGDHV O86869 159 68 -
YIKRVVGVGGDHV O69884 120 37 -
LIKRVIGLPGETI O07560 73 33 -
YIKRCMGKPGDTV O84023 181 62 -
FIKRIVASEGDWV O04348 235 45 -
IVKRVIGMPGDTI LEP_STRPN 74 30 -
MVKRVVAVGGDTV O69887 100 33 -
MVKRVVAVGGDTV O86870 100 33 -
LVKRIVALPGEKV O83896 175 82 -
ICKRVTGMPGDLV IMP1_YEAST 81 36 -
YVKRNFAIGGDEV O25300 104 60 -
QMRRVVGLPGDTV O83215 122 65 -
VCKRIIGMPGDTI O74800 78 37 -
YCKRVKGLPFDTI IMP2_YEAST 89 42 -
YTSRIIAKPGQSM LEPH_STAAU 73 32 -
KVSRIAAVQGDSV O51061 111 57 -

Motif 3 width=20
Element Seqn Id St Int Rpt
VPEGKYFVMGDNRQRSMDSR LEP_BACLI 138 41 -
VPAGHYFMMGDNRDNSNDSR LEP_PSEFL 216 60 -
VPDDKYFVMGDNRRNSMDSR LEPA_BACAM 137 41 -
VPKDKYFVMGDNRQESMDSR LEPP_BACNA 138 41 -
VPPGQYFMMGDNRDNSADSR LEP_ECOLI 264 107 -
VPAGHFFMMGDNRDNSTDSR O69160 185 69 -
VPKGKYFVMGDNRLNSMDSR LEP_BACAM 145 41 -
VPKGKYFVMGDNRLNSMDSR LEPT_BACSU 145 41 -
VPKDKYFVMGDNRQNSMDSR LEPQ_BACNA 137 41 -
VPDNKYFVMGDNRRNSMDSR LEPS_BACSU 136 42 -
VPPGQYFMMGDNRDNSADSR LEP_SALTY 264 107 -
VPAGHLFVLGDNRDNSADSR Q45225 186 64 -
VPEGQYFVMGDHRDHSDDSR LEP_HAEIN 288 81 -
VPDGQVFVMGDNRNNSNDSH P72660 136 31 -
VPEGKIWVMGDHRQNSRDSR O69886 234 39 -
VPEGKIWVMGDHRQNSRDSR O54237 189 39 -
VPDDQYLVLGDNRNNSYDSH P73157 142 31 -
VPPGRVWVMGDNRTHSADSR LEP_MYCTU 228 43 -
VPQGRLWVMGDNRIHSADSR O33021 216 43 -
VPEGYYFVMGDNRDNSQDSR O67088 178 92 -
IPKGKYLVLGDNREVSKDSR LEP_STAAU 137 49 -
VPPGCIFVLGDNRLSSWDSR LEPC_BACCL 135 45 -
VPADSFLVLGDNRNNSYDSH LEP_PHOLA 151 31 -
VPSGKYFVMGDNRLNSLDSR LEPU_BACSU 139 40 -
VPEGQYFFMGDNRDNSEDSR Q52697 198 82 -
VPEGRLWVMGDHRSNSADSR O69885 207 35 -
VPEGRLWVMGDHRSNSADSR O86869 207 35 -
VPDGTLFVLGDHRSDSSDSR O69884 169 36 -
VPKGKYFVVGDNRIYSFDSR O07560 131 45 -
IPEGHVLVLGDNCPMSADSR O84023 543 349 -
VPKGYVFVLGDNRNKSFDSH O04348 279 31 -
VPEGEYLLLGDDRLVSSDSR LEP_STRPN 158 71 -
VPEGRLFLLGDERRNSVDST O69887 148 35 -
VPEGRLFLLGDERRNSVDST O86870 148 35 -
LPEHNYFMMGDNRLNSTDMR O83896 441 253 -
VPEGHVWVTGDNLSHSLDSR IMP1_YEAST 120 26 -
INDDEFFMIGDNRDNSSDSR O25300 207 90 -
LDEHSYFVLCDNRIVSSDSR O83215 188 53 -
IPLGHVWLAGDNIAHSLDSR O74800 103 12 -
LPRGHIWVEGDNYFHSIDSN IMP2_YEAST 114 12 -
IPPNNFVVLNDHDNNQHDSR LEPH_STAAU 125 39 -
LKKNEFFLLNDNLSVLNDSR O51061 167 43 -