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PR00933

Identifier
BLYTICPTASE  [View Relations]  [View Alignment]  
Accession
PR00933
No. of Motifs
5
Creation Date
09-SEP-1998  (UPDATE 06-JUN-1999)
Title
B-lytic metalloendopeptidase (M23) signature
Database References

PROSITE; PS00142 ZINC_PROTEASE
BLOCKS; BL00142
INTERPRO; IPR000841
Literature References
1. RAWLINGS, N.D. AND BARRETT, A.J.
Evolutionary families of metallopeptidases.
METHODS ENZYMOL. 248 183-228 (1995).
 
2. RAWLINGS, N.D. AND BARRETT, A.J.
MEROPS - Peptidase Database
http://www.bi.bbsrc.ac.uk/merops/merops.htm
 
3. RAWLINGS, N.D. AND BARRETT, A.J.
Family M23 - Beta-Lytic metalloendopeptidase
http://www.bi.bbsrc.ac.uk/merops/famcards/m23.htm
 
4. LI, S.L., NORIOKA, S. AND SAKIYAMA, F.
Molecular cloning and nucleotide sequence of the beta-lytic protease gene
from Achromobacter lyticus. 
J.BACTERIOL. 172 6506-6511 (1990). 

Documentation
Metalloproteases are the most diverse of the four main types of protease,
with more than 30 families identified to date [1]. Of these, around
half contain the HEXXH motif, which has been shown in crystallographic
studies to form part of the metal-binding site [1]. The HEXXH motif is 
relatively common, but can be more stringently defined for metallo-
proteases as abXHEbbHbc, where a is most often valine or threonine and 
forms part of the S1' subsite in thermolysin and neprilysin, b is an
uncharged residue, and c a hydrophobic residue. Proline is never found
in this site, possibly because it would break the helical structure 
adopted by this motif in metalloproteases [1].
 
Metalloproteases can be split into five groups on the basis of their metal-
binding residues: the first three contain the HEXXH motif, the other two
do not [1]. In the first group, a glutamic acid completes the active site -
these are termed HEXXH+E: all families in this group show some sequence
relationship and have been assigned to clan MA [1]. The second group, which
have a third histidine as the extra metal-binding residue, are termed
HEXXH+H and are grouped into clan MB on the basis of their inter-relation-
ship[1]. In the third group, the additional metal-binding residues are
unidentified. The fourth group is diverse - the metal-binding residues are
known but do not form the HEXXH motif. And the fifth group comprises the
remaining families where the metal-binding residues are as yet unknown [1,2].
 
B-lytic endopeptidases are bacterial metallopeptidases that belong to the 
M23 protease family [1,3]. Cleavage is specific for glycine bonds,
especially in -Gly-Gly+Xaa sequences (Xaa is any aliphatic hydrophobic
residue). They lyse the cell walls of Gram-positive bacteria in which the
peptidoglycan cross-links contain glycine residues. The enzymes contain
zinc, but the exact position of the metal-binding ligands is uncertain. On
the basis of similarity with D-Ala-D-Ala-carboxypeptidase, it has been
suggested that a conserved His-X-His motif (where X is any amino acid)
forms part of the binding site [1].
 
The protein sequence deduced from the nucleotide sequence reveals a mature
enzyme of 179 residues [4]. In the gene product from Achromobacter lyticus,
an additional 195 amino acids at the N-terminal end of the protein include
the signal peptide, indicating that the enzyme is synthesised as a 
precursor [4]. 
 
BLYTICPTASE is a 5-element fingerprint that provides a signature for B-lytic
metalloendopeptidases (M23). The fingerprint was derived from an initial 
alignment of 3 sequences: the motifs were drawn from conserved regions 
spanning virtually the full length of the protease domain - motif 4 encodes
the putative di-histidine zinc binding site. Two iterations on OWL30.2 were
required to reach convergence, at which point a true set comprising 5 
sequences was identified. 
 
An update on SPTR37_9f identified a true set of 4 sequences.
Summary Information
4 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
544444
400000
300000
200000
12345
True Positives
LASA_PSEAE    P72165        PRLB_ACHLY    PRLB_LYSEN    
Sequence Titles
LASA_PSEAE  LASA PROTEASE PRECURSOR (EC 3.4.24.-) - PSEUDOMONAS AERUGINOSA. 
P72165 STAPHYLOLYTIC PROTEASE PREPROENZYME LASA PRECURSOR - PSEUDOMONAS AERUGINOSA.
PRLB_ACHLY BETA-LYTIC METALLOENDOPEPTIDASE PRECURSOR (EC 3.4.24.32) (BETA-LYTIC PROTEASE) - ACHROMOBACTER LYTICUS.
PRLB_LYSEN BETA-LYTIC METALLOENDOPEPTIDASE (EC 3.4.24.32) (BETA-LYTIC PROTEASE) - LYSOBACTER ENZYMOGENES.
Scan History
OWL30_2    2  50   NSINGLE    
SPTR37_9f 2 5 NSINGLE
Initial Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
QLPWRQGYSWQPNGAHSNTGSG LASA_PSEAE 196 196 -
QFPFPRGASWHVGGAHTNTGSG PRLB_ACHLY 202 202 -
QFPFPRGASWHVGGAHTNTGSG PRLB_LYSEN 7 7 -

Motif 2 width=19
Element Seqn Id St Int Rpt
YPYSSFDASYDWPRWGSAT LASA_PSEAE 218 0 -
YPMSSLDMSRGGGWGSNQN PRLB_ACHLY 225 1 -
YPMSSLDMSRGGGSNQNGN PRLB_LYSEN 30 1 -

Motif 3 width=19
Element Seqn Id St Int Rpt
GTVRVLSRCQVRVTHPSGW LASA_PSEAE 245 8 -
GSFKRHSSCFAEIVHTGGW PRLB_ACHLY 253 9 -
GSFKRHSSCFAEIVHTGGW PRLB_LYSEN 57 8 -

Motif 4 width=21
Element Seqn Id St Int Rpt
ALCEGGSSTGPHLHFSLLYNG LASA_PSEAE 297 33 -
ALCNGGQSTGPHEHWSLKQNG PRLB_ACHLY 305 33 -
ALCNGGQSTGPHQHWSLKQNG PRLB_LYSEN 109 33 -

Motif 5 width=24
Element Seqn Id St Int Rpt
GASFGPYRINVGTSNYDNDCRRYY LASA_PSEAE 324 6 -
GTYLSGYRITATGSSYDTNCSRFY PRLB_ACHLY 332 6 -
GTYLSGYRITATGSSYDTNCSRFY PRLB_LYSEN 136 6 -
Final Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
QLPWRQGYSWQPNGAHSNTGSG LASA_PSEAE 196 196 -
QLPWRQGYSWQPNGAHSNTGSG P72165 244 244 -
QFPFPRGASWHVGGAHTNTGSG PRLB_ACHLY 202 202 -
QFPFPRGASWHVGGAHTNTGSG PRLB_LYSEN 7 7 -

Motif 2 width=19
Element Seqn Id St Int Rpt
YPYSSFDASYDWPRWGSAT LASA_PSEAE 218 0 -
YPYSSFDASYDWPRWGSAT P72165 266 0 -
YPMSSLDMSRGGGWGSNQN PRLB_ACHLY 225 1 -
YPMSSLDMSRGGGSNQNGN PRLB_LYSEN 30 1 -

Motif 3 width=19
Element Seqn Id St Int Rpt
GTVRVLSRCQVRVTHPSGW LASA_PSEAE 245 8 -
GTVRVLSRCQVRVTHPSGW P72165 293 8 -
GSFKRHSSCFAEIVHTGGW PRLB_ACHLY 253 9 -
GSFKRHSSCFAEIVHTGGW PRLB_LYSEN 57 8 -

Motif 4 width=21
Element Seqn Id St Int Rpt
ALCEGGSSTGPHLHFSLLYNG LASA_PSEAE 297 33 -
ALCEGGSSTGPHLHFSLLYNG P72165 345 33 -
ALCNGGQSTGPHEHWSLKQNG PRLB_ACHLY 305 33 -
ALCNGGQSTGPHQHWSLKQNG PRLB_LYSEN 109 33 -

Motif 5 width=24
Element Seqn Id St Int Rpt
GASFGPYRINVGTSNYDNDCRRYY LASA_PSEAE 324 6 -
GASFGPYRINVGTSNYDNDCRRYY P72165 372 6 -
GTYLSGYRITATGSSYDTNCSRFY PRLB_ACHLY 332 6 -
GTYLSGYRITATGSSYDTNCSRFY PRLB_LYSEN 136 6 -