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PR00922

Identifier
DADACBPTASE3  [View Relations]  [View Alignment]  
Accession
PR00922
No. of Motifs
5
Creation Date
21-JUN-1998  (UPDATE 28-JUL-1999)
Title
D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
Database References

INTERPRO; IPR000667
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. BAIROCH, A. AND RAWLINGS, N.
Classification of peptidase families and index of peptidase entries in
SWISS-PROT.
http://expasy.hcuge.ch/cgi-bin/lists?peptidas.txt
 
4. GHUYSEN J-M.
Serine beta-lactamases and penicillin-binding proteins.
ANNU.REV.MICROBIOL. 45 37-67 (1991).

Documentation
Proteolytic enzymes that use serine in their catalytic machinery are 
widespread and numerous, being found in viruses, bacteria and eukaryotes
[1]. They encompass a range of peptidase activity, including exopeptidase,
endopeptidase, oligopeptidase and omega-peptidase. More than 20 serine
protease families (denoted S1 - S27) have been identified, which have been
grouped into 6 clans (SA, SB, SC, SE, SF and SG) on the basis of structural
and functional similarities [1]. Structures from four clans have been
examined (SA, SB, SC and SE): these appear to be unrelated, suggesting at 
least four evolutionary origins of serine peptidase, and possibly many more
[1]. Since that examination, structural representations from the other two 
clan members (SF, SG) have been determined [3].
 
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].
 
D-Ala-D-Ala carboxypeptidase (clan SE) is involved in the metabolism of 
cell components [4]; 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 (designated S11, S12 and S13),
which are also known as low molecular weight penicillin-binding proteins [1].
 
Family S13 comprises D-Ala-D-Ala peptidases that have sufficient sequence
similarity around their active sites to assume a distant evolutionary
relationship to other clan members; members of the S13 family also bind
penicilin and have D-amino-peptidase activity. Proteases of family S11 have
exclusive D-Ala-D-Ala peptidase activity, while some members of S12 are 
C beta-lactamases [1]. 
 
DADACBPTASE3 is a 5-element fingerprint that provides a signature for the
D-Ala-D-Ala carboxypeptidase 1 (S13) family of serine proteases. The 
fingerprint was derived from an initial alignment of 7 sequences: the 
motifs were drawn from conserved regions surrounding the active site - 
motif 1 contains the catalytic Ser, and Lys residues; motifs 2 and 3 include
Ser and Asp residues, both of which have been implicated in the catalytic
mechanism of the related beta-lactamase A. A single iteration on OWL30.1
was required to reach convergence, no further sequences being identified 
beyond the starting set.
 
An update on SPTR37_9f identified a true set of 9 sequences, and 1
partial match.
Summary Information
   9 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
599999
400000
300000
201001
12345
True Positives
DAC_ACTSP     O06380        O69539        O85665        
P74032 PBP4_ECOLI PBP4_HAEIN PBP_BACSU
Q55728
True Positive Partials
Codes involving 2 elements
P74173
Sequence Titles
DAC_ACTSP   D-ALANYL-D-ALANINE CARBOXYPEPTIDASE PRECURSOR (EC 3.4.16.4) (DD- PEPTIDASE) (DD-CARBOXYPEPTIDASE) - ACTINOMADURA SP. (STRAIN R39). 
O06380 HYPOTHETICAL 46.8 KD PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
O69539 HYPOTHETICAL 47.2 KD PROTEIN - MYCOBACTERIUM LEPRAE.
O85665 PENICILLIN BINDING PROTEIN 3 - NEISSERIA GONORRHOEAE.
P74032 D-ALANYL-D-ALANINE CARBOXYPEPTIDASE - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
PBP4_ECOLI PENICILLIN-BINDING PROTEIN 4 PRECURSOR (PBP-4) [INCLUDES: D-ALANYL-D- ALANINE CARBOXYPEPTIDASE (EC 3.4.16.4) (DD-PEPTIDASE) (DD- CARBOXYPEPTIDASE); D-ALANYL-D-ALANINE-ENDOPEPTIDASE (EC 3.4.99.-) (DD- ENDOPEPTIDASE)] - ESCHERICHIA COLI.
PBP4_HAEIN PENICILLIN-BINDING PROTEIN 4 PRECURSOR (PBP-4) [INCLUDES: D-ALANYL-D- ALANINE CARBOXYPEPTIDASE (EC 3.4.16.4) (DD-PEPTIDASE) (DD- CARBOXYPEPTIDASE); D-ALANYL-D-ALANINE-ENDOPEPTIDASE (EC 3.4.99.-) (DD- ENDOPEPTIDASE)] - HAEMOPHILUS INFLUENZAE.
PBP_BACSU PUTATIVE PENICILLIN BINDING PROTEIN PRECURSOR - BACILLUS SUBTILIS.
Q55728 PENICILLIN-BINDING PROTEIN 4 - SYNECHOCYSTIS SP. (STRAIN PCC 6803).

P74173 HYPOTHETICAL 46.4 KD PROTEIN - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
Scan History
OWL30_1    1  100  NSINGLE    
SPTR37_9f 2 100 NSINGLE
Initial Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
FIPASNQKLITTAMALQELG S76523 86 86 -
LVPASTNKILTAAAALLTLD MTY15C1024 110 110 -
FIPASNAKIFTTAAALQRLG S75544 122 122 -
LLPASNMKLFTAAAALEVLG DAC_ACTSP 94 94 -
ALPASTQKVITALAALIQLG PBP4_ECOLI 58 58 -
MLSASTQKVFTAVAAKLALD PBP4_HAEIN 65 65 -
MRPASSLKLLTAAAALSVLG PBP_BACSU 77 77 -

Motif 2 width=23
Element Seqn Id St Int Rpt
VVASKQSAPLHDLLKIMLKKSDN PBP4_ECOLI 286 208 -
VLADHTSAELSEILVPFMKFSNN DAC_ACTSP 327 213 -
PNATVRSQPLRNWVMTTNKRSNN S75544 142 0 -
QLAVVQSAPLIQRLSQMMNASDN MTY15C1024 275 145 -
APAPLLALTSPPLWTLIKTVNQD S76523 302 196 -
VLLSHRSMPLSKLFVPFMKLSNN PBP_BACSU 308 211 -
LLAKHLSKPLPDLLKKMMKKSDN PBP4_HAEIN 290 205 -

Motif 3 width=15
Element Seqn Id St Int Rpt
GLATTTVRLRDGSGL S76523 354 29 -
GVNPQGFRVADGSGL S75544 188 23 -
GVDTAGLVLNDGSGL DAC_ACTSP 384 34 -
GVDIGNTIIADGSGL PBP4_ECOLI 345 36 -
GIRFGNSILADGSGL PBP4_HAEIN 348 35 -
GVDSKSLVLRDGSGI PBP_BACSU 365 34 -
HIDTAGAALVDSSGL MTY15C1024 332 34 -

Motif 4 width=15
Element Seqn Id St Int Rpt
SRHNLIAPATMMQVL PBP4_ECOLI 360 0 -
SRHNLVAPKTMLSVL PBP4_HAEIN 363 0 -
SHIDAVSSDQLSQLL PBP_BACSU 380 0 -
SRNNAATPRSLVDTL S75544 203 0 -
SLDNRLTARTLDATM MTY15C1024 347 0 -
SRQDLVTPQALVQLL S76523 369 0 -
SRGNLVTADTVVDLL DAC_ACTSP 399 0 -

Motif 5 width=14
Element Seqn Id St Int Rpt
VRALSGYANTPAHG S75544 265 47 -
VVSLTGYVENQQWG S76523 431 47 -
VYNLAGFITTASGQ PBP4_ECOLI 424 49 -
VYNLAGFMTNARGE PBP4_HAEIN 427 49 -
VSSLSGYAETKSGK PBP_BACSU 447 52 -
VSALSGYVPGPEGE DAC_ACTSP 466 52 -
AINSLVGVLTDRSG MTY15C1024 414 52 -
Final Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
LLPASNMKLFTAAAALEVLG DAC_ACTSP 94 94 -
ALPASTQKVITALAALIQLG PBP4_ECOLI 58 58 -
MLSASTQKVFTAVAAKLALD PBP4_HAEIN 65 65 -
LVPASTNKILTAAAALLTLD O06380 110 110 -
FIPASNAKIFTTAAALQRLG P74032 122 122 -
LVPASANKLLTAAAALLTLD O69539 110 110 -
MRPASSLKLLTAAAALSVLG PBP_BACSU 77 77 -
VNPASTMKLVTAFAAFKTFG O85665 54 54 -
FIPASNQKLITTAMALQELG Q55728 86 86 -

Motif 2 width=23
Element Seqn Id St Int Rpt
VLADHTSAELSEILVPFMKFSNN DAC_ACTSP 327 213 -
VVASKQSAPLHDLLKIMLKKSDN PBP4_ECOLI 286 208 -
LLAKHLSKPLPDLLKKMMKKSDN PBP4_HAEIN 290 205 -
QLAVVQSAPLIQRLSQMMNASDN O06380 275 145 -
PNATVRSQPLRNWVMTTNKRSNN P74032 142 0 -
QLAVVQSAPLVQRLSEMMDNSDN O69539 275 145 -
VLLSHRSMPLSKLFVPFMKLSNN PBP_BACSU 308 211 -
TLAVAHSKPMKEILTDMNKRSDN O85665 279 205 -
PLLALTSPPLWTLIKTVNQDSNN Q55728 305 199 -

Motif 3 width=15
Element Seqn Id St Int Rpt
GVDTAGLVLNDGSGL DAC_ACTSP 384 34 -
GVDIGNTIIADGSGL PBP4_ECOLI 345 36 -
GIRFGNSILADGSGL PBP4_HAEIN 348 35 -
HIDTAGAALVDSSGL O06380 332 34 -
GVNPQGFRVADGSGL P74032 188 23 -
HIDTTGAALVDSSGL O69539 332 34 -
GVDSKSLVLRDGSGI PBP_BACSU 365 34 -
GIDVADLVLENGSGL O85665 336 34 -
GLATTTVRLRDGSGL Q55728 354 26 -

Motif 4 width=15
Element Seqn Id St Int Rpt
SRGNLVTADTVVDLL DAC_ACTSP 399 0 -
SRHNLIAPATMMQVL PBP4_ECOLI 360 0 -
SRHNLVAPKTMLSVL PBP4_HAEIN 363 0 -
SLDNRLTARTLDATM O06380 347 0 -
SRNNAATPRSLVDTL P74032 203 0 -
SVNNRLTAKTLGGAV O69539 347 0 -
SHIDAVSSDQLSQLL PBP_BACSU 380 0 -
SRKERVTARMMAQIL O85665 351 0 -
SRQDLVTPQALVQLL Q55728 369 0 -

Motif 5 width=14
Element Seqn Id St Int Rpt
VSALSGYVPGPEGE DAC_ACTSP 466 52 -
VYNLAGFITTASGQ PBP4_ECOLI 424 49 -
VYNLAGFMTNARGE PBP4_HAEIN 427 49 -
AINSLVGVLTDRSG O06380 414 52 -
VRALSGYANTPAHG P74032 265 47 -
AINSLVGVVTDRSG O69539 414 52 -
VSSLSGYAETKSGK PBP_BACSU 447 52 -
VRALAGYWLGDKPM O85665 411 45 -
VVSLTGYVENQQWG Q55728 431 47 -