| 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).
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| 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.
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| 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).
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