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PR00725

Identifier
DADACBPTASE1  [View Relations]  [View Alignment]  
Accession
PR00725
No. of Motifs
3
Creation Date
10-MAY-1997  (UPDATE 24-JUN-1999)
Title
D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
Database References

PFAM; PF00768 Peptidase_S11
INTERPRO; IPR001967
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).
 
3. GHUYSEN J-M.
Serine beta-lactamases and penicillin-binding proteins.
ANNU.REV.MICROBIOL. 45 37-67 (1991).
 
4. PALOMEQUE-MESSIA, ENGELBERT, S., LEYH-BOUILLE, M., NGUYEN-DISTECHE, M.,
DUEZ, C., HOUBA, S., DIDEBERG, O., VAN BEEUMEN, J. AND GHUYSEN, J-M.
Amino acid sequence of the penicillin-binding protein/DD-peptidase of
Streptomyces K15. Predicted secondary structures of the low Mr penicillin-
binding proteins of class A.
BIOCHEM.J. 279 223-230 (1991).

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 - S27) 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].
 
Bacterial cell walls are complex structures containing amino acids and 
amino sugars, with alternating chains of N-acetylglucosamine and N-acetyl-
muramic acid units linked by short peptides [1]: the link peptide in E.coli
is L-alanyl-D-isoglutamyl-L-meso-diaminopimelyl-D-alanine [1]. The chains
are usually cross-linked between the carboxyl of D-alanine and the free
amino group of diaminopimelate [1]. During the synthesis of peptidoglycan,
the precursor has the described tetramer sequence with an added C-terminal
D-alanine [1].
 
D-Ala-D-Ala carboxypeptidase is involved in the metabolism of cell 
components [3]; it is synthesised with a leader peptide to target it to 
the cell membrane [1]. After cleavage of the leader peptide, the enzyme is 
retained in the membrane by a C-terminal anchor [1]. There are three
families of serine-type D-Ala-D-Ala peptidase, which are also known as
low molecular weight penicillin-binding proteins [1].
 
Family S11 contains only D-Ala-D-Ala peptidases, unlike families S12 and S13,
which contain other enzymes, such as class C beta-lactamases and D-amino-
peptidases [1]. Although these enzymes are serine proteases, some members
of family S11 are partially inhibited by thiol-blocking agents [4].
 
DADACBPTASE1 is a 3-element fingerprint that provides a signature for the
D-Ala-D-Ala carboxypeptidase 1 (S11) family of serine proteases. The 
fingerprint was derived from an initial alignment of 8 sequences: the motifs
were largely drawn from conserved regions surrounding the active site -
motif 1 contains the catalytic Ser and Lys residues; and motif 2 includes
a Ser residue that has been implicated in catalysis in the related protein
beta-lactamase A. Three iterations on OWL29.2 were required to reach
convergence, at which point a true set comprising 21 sequences was
identified. A single partial match was also found, CPDACF, a fragment 
lacking the portion of sequence bearing motif 1.
 
An update on SPTR37_9f identified a true set of 22 sequences, and 1
partial match.
Summary Information
  22 codes involving  3 elements
1 codes involving 2 elements
Composite Feature Index
3222222
2110
123
True Positives
DACA_BACST    DACA_BACSU    DACA_ECOLI    DACA_HAEIN    
DACB_BACSU DACC_ECOLI DACD_ECOLI DACD_SALTY
DACF_BACSU DACX_STRSK O51550 O54201
O83778 P72355 P72518 PBP5_PSEAE
PBP7_ECOLI PBP7_HAEIN Q10828 Q53613
Q54906 Q57540
True Positive Partials
Codes involving 2 elements
O84555
Sequence Titles
DACA_BACST  D-ALANYL-D-ALANINE CARBOXYPEPTIDASE PRECURSOR (EC 3.4.16.4) (DD- PEPTIDASE) (DD-CARBOXYPEPTIDASE) (CPASE) (PBP5) - BACILLUS STEAROTHERMOPHILUS. 
DACA_BACSU D-ALANYL-D-ALANINE CARBOXYPEPTIDASE PRECURSOR (EC 3.4.16.4) (DD- PEPTIDASE) (DD-CARBOXYPEPTIDASE) (CPASE) (PBP5) - BACILLUS SUBTILIS.
DACA_ECOLI PENICILLIN-BINDING PROTEIN 5 PRECURSOR (D-ALANYL-D-ALANINE CARBOXYPEPTIDASE FRACTION A) (EC 3.4.16.4) (DD-PEPTIDASE) (DD-CARBOXYPEPTIDASE) (PBP-5) - ESCHERICHIA COLI.
DACA_HAEIN PENICILLIN-BINDING PROTEIN 5 PRECURSOR (D-ALANYL-D-ALANINE CARBOXYPEPTIDASE FRACTION A) (EC 3.4.16.4) (DD-PEPTIDASE) (DD-CARBOXYPEPTIDASE) (PBP-5) - HAEMOPHILUS INFLUENZAE.
DACB_BACSU PENICILLIN-BINDING PROTEIN 5* PRECURSOR (D-ALANYL-D-ALANINE CARBOXYPEPTIDASE) (EC 3.4.16.4) (DD-PEPTIDASE) (DD-CARBOXYPEPTIDASE) (PBP-5*) - BACILLUS SUBTILIS.
DACC_ECOLI PENICILLIN-BINDING PROTEIN 6 PRECURSOR (D-ALANYL-D-ALANINE CARBOXYPEPTIDASE FRACTION C) (EC 3.4.16.4) (DD-PEPTIDASE) (DD-CARBOXYPEPTIDASE) (PBP-6) - ESCHERICHIA COLI.
DACD_ECOLI PENICILLIN-BINDING PROTEIN 6B PRECURSOR (D-ALANYL-D-ALANINE CARBOXYPEPTIDASE) (EC 3.4.16.4) (DD-PEPTIDASE) (DD-CARBOXYPEPTIDASE) (PBP-6B) - ESCHERICHIA COLI.
DACD_SALTY PENICILLIN-BINDING PROTEIN 6B PRECURSOR (D-ALANYL-D-ALANINE CARBOXYPEPTIDASE) (EC 3.4.16.4) (DD-PEPTIDASE) (DD-CARBOXYPEPTIDASE) (PBP-6B) - SALMONELLA TYPHIMURIUM.
DACF_BACSU PENICILLIN-BINDING PROTEIN DACF PRECURSOR (D-ALANYL-D-ALANINE CARBOXYPEPTIDASE) (EC 3.4.16.4) (DD-PEPTIDASE) (DD-CARBOXYPEPTIDASE) - BACILLUS SUBTILIS.
DACX_STRSK D-ALANYL-D-ALANINE CARBOXYPEPTIDASE PRECURSOR (EC 3.4.16.4) (DD- PEPTIDASE) (DD-CARBOXYPEPTIDASE) - STREPTOMYCES SP. (STRAIN K15).
O51550 SERINE-TYPE D-ALA-D-ALA CARBOXYPEPTIDASE (DACA) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O54201 PBP2 PROTEIN (PENICILLIN BINDING PROTEIN PBPA) - STREPTOMYCES CLAVULIGERUS.
O83778 SERINE-TYPE D-ALA-D-ALA CARBOXYPEPTIDASE (DACC) - TREPONEMA PALLIDUM.
P72355 PENICILLIN-BINDING PROTEIN 4 - STAPHYLOCOCCUS AUREUS.
P72518 PENICILLIN-BINDING PROTEIN 3 PRECURSOR (D-ALANYL-D-ALANINE CARBOXYPEPTIDASE) (EC 3.4.16.4) (DD-PEPTIDASE) (DD-CARBOXYPEPTIDASE) (PBP-3) - STREPTOCOCCUS PNEUMONIAE.
PBP5_PSEAE PENICILLIN-BINDING PROTEIN 5 PRECURSOR (PBP-5) (D-ALANYL-D-ALANINE- ENDOPEPTIDASE) (EC 3.4.99.-) (DD-ENDOPEPTIDASE) - PSEUDOMONAS AERUGINOSA.
PBP7_ECOLI PENICILLIN-BINDING PROTEIN 7 PRECURSOR (PBP-7) (D-ALANYL-D-ALANINE- ENDOPEPTIDASE) (EC 3.4.99.-) (DD-ENDOPEPTIDASE) - ESCHERICHIA COLI.
PBP7_HAEIN PENICILLIN-BINDING PROTEIN 7 HOMOLOG PRECURSOR (PBP-7) (D-ALANYL-D- ALANINE-ENDOPEPTIDASE) (EC 3.4.99.-) (DD-ENDOPEPTIDASE) - HAEMOPHILUS INFLUENZAE.
Q10828 PROBABLE PENICILLIN-BINDING PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
Q53613 PENCILLIN BINDING PROTEIN 4 - STAPHYLOCOCCUS AUREUS.
Q54906 PENICILLIN-BINDING PROTEIN - STREPTOCOCCUS PYOGENES.
Q57540 PENICILLIN BINDING PROTEIN 4 - STAPHYLOCOCCUS AUREUS.

O84555 D-ALA-D-ALA CARBOXYPEPTIDASE - CHLAMYDIA TRACHOMATIS.
Scan History
OWL29_2    3  100  NSINGLE    
SPTR37_9f 2 50 NSINGLE
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
ASLTKIMTSYVV DACC_ECOLI 65 65 -
ASMTKMMTEYLL DACA_BACSU 66 66 -
ASMTKIMTMLLI DACF_BACSU 63 63 -
ASITKIMTAVLA DACB_BACSU 59 59 -
ASMTKMMTEYLL DACA_BACST 65 65 -
ASLTKMMTSYVI DACA_ECOLI 72 72 -
GSTTKIMTAKVV DACX_STRSK 63 63 -
ASISKLMTAMVV PBP7_ECOLI 69 69 -

Motif 2 width=18
Element Seqn Id St Int Rpt
LNKGVIIQSGNDACIALA DACC_ECOLI 124 47 -
LYQATAIYSANAAAIAIA DACA_BACSU 123 45 -
MLKGIAIASGNDASVAMA DACF_BACSU 116 41 -
LVYGLMLRSGNDAAVAIA DACB_BACSU 107 36 -
LYEAMAIYSANGATVAIA DACA_BACST 122 45 -
LIRGINLQSGNDACVAMA DACA_ECOLI 131 47 -
LLYGLMLPSGCDAAYALA DACX_STRSK 117 42 -
MLLLALMSSENRAAASLA PBP7_ECOLI 119 38 -

Motif 3 width=14
Element Seqn Id St Int Rpt
FIGLMNGYAKKLGL DACC_ECOLI 151 9 -
FVEKMNAKAKELGL DACA_BACSU 150 9 -
FVKKMNKKAKELGL DACF_BACSU 143 9 -
FVYMMNQKAEQLGM DACB_BACSU 134 9 -
FVKMMNDKAKELGL DACA_BACST 149 9 -
FVGLMNSYVNALGL DACA_ECOLI 158 9 -
FIGKMNTAATNLGL DACX_STRSK 150 15 -
FIKAMNAKAKSLGM PBP7_ECOLI 146 9 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
ASLTKIMTSYVV DACC_ECOLI 65 65 -
ASLTKLMTGYVV DACD_ECOLI 62 62 -
ASMTKLMTMYLT Q57540 74 74 -
ASMTKLMTMYLT Q53613 74 74 -
ASMTKLMTMYLT P72355 74 74 -
ASLTKLMTGYVV DACD_SALTY 64 64 -
ASMTKMMTEYLL DACA_BACSU 66 66 -
ASMTKIMTMLLI DACF_BACSU 63 63 -
ASITKIMTAVLA DACB_BACSU 59 59 -
ASLTKMMTSYVV DACA_HAEIN 64 64 -
ASMTKMMTEYLL DACA_BACST 65 65 -
ASITKLMTAMVV PBP5_PSEAE 65 65 -
ASLTKMMTSYVI DACA_ECOLI 72 72 -
ASVTKLMTANVF PBP7_HAEIN 44 44 -
GSTTKIMTAKVV DACX_STRSK 63 63 -
ASISKLMTAMVV PBP7_ECOLI 69 69 -
ASITKLITVYLV P72518 55 55 -
ASTAKIMTAYVL O54201 364 364 -
ASLTKIVTIYTA O51550 66 66 -
ASLAKLVTCAVV O83778 124 124 -
ASTIKVLLALVA Q10828 68 68 -
ASVSKLLTTYLV Q54906 55 55 -

Motif 2 width=18
Element Seqn Id St Int Rpt
LNKGVIIQSGNDACIALA DACC_ECOLI 124 47 -
LSRGLIVDSGNDACVALA DACD_ECOLI 121 47 -
LLQITVSNSSNAAALILA Q57540 131 45 -
LLQITVSNSSNAAALILA Q53613 131 45 -
LLQITVSNSSNAAALILA P72355 131 45 -
LSRGLIVDSGNDACVALA DACD_SALTY 123 47 -
LYQATAIYSANAAAIAIA DACA_BACSU 123 45 -
MLKGIAIASGNDASVAMA DACF_BACSU 116 41 -
LVYGLMLRSGNDAAVAIA DACB_BACSU 107 36 -
LNRGVIVVSGNDATVALA DACA_HAEIN 120 44 -
LYEAMAIYSANGATVAIA DACA_BACST 122 45 -
MLLLALMSSENRAAASLA PBP5_PSEAE 115 38 -
LIRGINLQSGNDACVAMA DACA_ECOLI 131 47 -
LLKAMLVHSDNYAAHALS PBP7_HAEIN 94 38 -
LLYGLMLPSGCDAAYALA DACX_STRSK 117 42 -
MLLLALMSSENRAAASLA PBP7_ECOLI 119 38 -
LLEATLVSSANSAAIALA P72518 111 44 -
MLKMLMIPSGNNIGRLLA O54201 422 46 -
ILKGLSVSSGNDSSIAIA O51550 123 45 -
LLAGMNIASGNDAAYTLA O83778 181 45 -
LLDGLLLVSGNDAANTLA Q10828 116 36 -
LLSALVVNNANSPAIALA Q54906 111 44 -

Motif 3 width=14
Element Seqn Id St Int Rpt
FIGLMNGYAKKLGL DACC_ECOLI 151 9 -
FVEMMNNYAEKLHL DACD_ECOLI 148 9 -
FVDLMNNKAKAIGM Q57540 158 9 -
FVDLMNNKAKAIGM Q53613 158 9 -
FVDLMNNKAKAIGM P72355 158 9 -
FVAMMNSYVKKLNL DACD_SALTY 150 9 -
FVEKMNAKAKELGL DACA_BACSU 150 9 -
FVKKMNKKAKELGL DACF_BACSU 143 9 -
FVYMMNQKAEQLGM DACB_BACSU 134 9 -
FVETMNKYVQQFGL DACA_HAEIN 147 9 -
FVKMMNDKAKELGL DACA_BACST 149 9 -
FVKAMNAKAHALGM PBP5_PSEAE 142 9 -
FVGLMNSYVNALGL DACA_ECOLI 158 9 -
FIKKMNEKAHQLGM PBP7_HAEIN 121 9 -
FIGKMNTAATNLGL DACX_STRSK 150 15 -
FIKAMNAKAKSLGM PBP7_ECOLI 146 9 -
FVDMMRAKLLEWGI P72518 138 9 -
FVREMNEAAKDLGM O54201 451 11 -
FVNLMNINVLNLGL O51550 150 9 -
FCTRMNTLVQKWGL O83778 208 9 -
TVAKMNAKAATLGA Q10828 142 8 -
FVDKMKKQLRQWGI Q54906 138 9 -