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PR00728

Identifier
SIGNALPTASE  [View Relations]  [View Alignment]  
Accession
PR00728
No. of Motifs
2
Creation Date
11-MAY-1997  (UPDATE 28-JUN-1999)
Title
Eukaryotic signal peptidase (S26B) family signature
Database References

PROSITE; PS00501 SPASE_I_1; PS00761 SPASE_I_3
BLOCKS; BL00501
PFAM; PF00461 Peptidase_S26
INTERPRO; IPR001733
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].
 
Eukaryotic microsomal signal peptidase is involved in the removal of signal
peptides from secretory proteins as they pass into the endoplasmic reticulum
lumen [1]. The peptidase is more complex than its mitochondrial and
bacterial counterparts, containing a number of subunits, ranging from two
in the chicken oviduct peptidase, to five in the dog pancreas protein [1].
A number of these have been shown to be similar and form the eukaryotic
signal peptidase (S26) family. They share sequence similarity with the
bacterial leader peptidases (family S26A), although activity here is mediated
by a serine/histidine dyad rather than a serine/lysine dyad [1].
 
SIGNALPTASE is a 2-element fingerprint that provides a signature for the
eukaryotic signal peptidase (S26B) family. The fingerprint was derived from
an inital alignment of 5 sequences: the motifs were drawn from conserved
regions within the putative lumenal domain - motif 1 includes the region
encoded by PROSITE pattern SPASE_I_1 (PS00501), which contains the active
serine; and motif 2 includes the region encoded by PROSITE pattern SPASE_I_3
(PS00760), a conserved region of unknown function (the region surrounding
the proposed active His was not sufficiently well conserved to be used as
a diagnostic motif). Two iterations on OWL29.3 were required to reach
convergence, at which point a true set comprising 7 sequences was identified.
 
An update on SPTR37_9f identified a true set of 12 sequences.
Summary Information
12 codes involving  2 elements
Composite Feature Index
21212
12
True Positives
LEPW_BACSU    O27497        O28201        O28616        
O28618 O58298 O58327 O74323
SC11_YEAST SPC3_CANFA SPC4_CANFA SPC4_RAT
Sequence Titles
LEPW_BACSU  SIGNAL PEPTIDASE I W (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDASE I) - BACILLUS SUBTILIS. 
O27497 SIGNAL PEPTIDASE - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O28201 HYPOTHETICAL 38.1 KD PROTEIN - ARCHAEOGLOBUS FULGIDUS.
O28616 SIGNAL SEQUENCE PEPTIDASE (SPC21) - ARCHAEOGLOBUS FULGIDUS.
O28618 SIGNAL SEQUENCE PEPTIDASE, PUTATIVE - ARCHAEOGLOBUS FULGIDUS.
O58298 330AA LONG HYPOTHETICAL PROTEIN - PYROCOCCUS HORIKOSHII.
O58327 154AA LONG HYPOTHETICAL SIGNAL PEPTIDASE SUBUNIT - PYROCOCCUS HORIKOSHII.
O74323 PUTATIVE SIGNAL SEQUENCE PROCESSING PROTEIN, PEPTIDASE - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
SC11_YEAST SIGNAL SEQUENCE PROCESSING PROTEIN SEC11 (EC 3.4.-.-) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
SPC3_CANFA MICROSOMAL SIGNAL PEPTIDASE 21 KD SUBUNIT (EC 3.4.-.-) (SPC21) - CANIS FAMILIARIS (DOG).
SPC4_CANFA MICROSOMAL SIGNAL PEPTIDASE 18 KD SUBUNIT (EC 3.4.-.-) (SPC18) - CANIS FAMILIARIS (DOG).
SPC4_RAT MICROSOMAL SIGNAL PEPTIDASE 18 KD SUBUNIT (EC 3.4.-.-) (SPC18) - RATTUS NORVEGICUS (RAT).
Scan History
OWL29_3    2  100  NSINGLE    
SPTR37_9f 2 100 NSINGLE
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
VLSGSMEPEFNTGSLI YQHE_BACSU 43 43 -
VLSGSMEPAFHRGDLL SPC4_RAT 52 52 -
VLSGSMEPAFHRGDLL SPC4_CANFA 52 52 -
VLSGSMEPAFHRGDLL SPC3_CANFA 63 63 -
VLSGSMEPAFQRGDIL SC11_YEAST 40 40 -

Motif 2 width=12
Element Seqn Id St Int Rpt
LLTKGDNNAGND SC11_YEAST 98 42 -
FKTKGDNNAAAD YQHE_BACSU 101 42 -
FLTKGDNNAVDD SPC4_RAT 111 43 -
FLTKGDNNAVDD SPC4_CANFA 111 43 -
FLTKGDNNEVDD SPC3_CANFA 122 43 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
VLSGSMEPAFHRGDLL SPC4_RAT 52 52 -
VLSGSMEPAFHRGDLL SPC4_CANFA 52 52 -
VLSGSMEPAFHRGDLL SPC3_CANFA 63 63 -
VLSGSMEPAFQRGDIL SC11_YEAST 40 40 -
VLSESMEPSFQRGDLL O74323 43 43 -
VVSGSMEPVFYRGDIV O27497 30 30 -
VLSGSMEPEFNTGSLI LEPW_BACSU 43 43 -
VVSGSMEPVFHRGDVV O58327 38 38 -
VTSDSMTPTLNRGDLF O28201 36 36 -
VLSSSMEPLMHPGDLI O28618 32 32 -
AYSDSMVPTINRWDVF O58298 34 34 -
TYGTSMLPELETGDLI O28616 28 28 -

Motif 2 width=12
Element Seqn Id St Int Rpt
FLTKGDNNAVDD SPC4_RAT 111 43 -
FLTKGDNNAVDD SPC4_CANFA 111 43 -
FLTKGDNNEVDD SPC3_CANFA 122 43 -
LLTKGDNNAGND SC11_YEAST 98 42 -
LITKGDNNKIDD O74323 118 59 -
YITKGDNNQDPD O27497 97 51 -
FKTKGDNNAAAD LEPW_BACSU 101 42 -
FITWGDHNPVPD O58327 100 46 -
YITKGDHNIATD O28201 86 34 -
FKTKGDAVEDVD O28618 86 38 -
YITKGDNNVATD O58298 84 34 -
IITKGDNLPRED O28616 84 40 -