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PR00726

Identifier
LEXASERPTASE  [View Relations]  [View Alignment]  
Accession
PR00726
No. of Motifs
3
Creation Date
20-MAY-1997  (UPDATE 27-JUN-1999)
Title
Repressor LexA serine protease (S24) family signature
Database References

PFAM; PF00717 Peptidase_S24
INTERPRO; IPR000129
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 - 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].
 
The lexA protein represses around 20 genes of the cellular SOS response to 
DNA damage in E.coli [1]. Damage to cellular DNA results in inactivation of
lexA, allowing transcription of the genes involved in DNA repair [1]. In 
E.coli, this derepression of the DNA repair system is effected by the recA
protein, which binds to lexA upon interaction with single-stranded 
DNA [1]. This results in inactivation of lexA by proteolytic cleavage,
disrupting the DNA-binding capabilities of lexA [1]. Although initially
thought to be mediated by recA, it has been found that the cleavage of lexA
is an autolytic event catalysed by the presence of recA [1].
 
The lexA protein consists of around 200 amino acids, of which the first 90 
form the DNA-binding domain [1]. The remaining residues form the protease 
domain, Ser-119 and Lys-156 being the active residues.
 
LEXASERPTASE is a 3-element fingerprint that provides a signature for the
protease domain of the lexA repressor and related proteins. The fingerprint
was derived from an initial alignment of 8 sequences: the motifs were drawn
from conserved regions spanning the C-terminal half of the alignment in the
vicinity of the active site -  motif 1 contains the catalytic serine,
and motif 3 the catalytic lysine. Two iterations on OWL29.3 were
required to reach convergence, at which point a true set comprising 17
sequences was identified. A single partial match was also found, RNU77699,
a fragment that shows a high degree of similarity to the first 2 motifs.
 
An update on SPTR37_9f identified a true set of 26 sequences.
Summary Information
26 codes involving  3 elements
0 codes involving 2 elements
Composite Feature Index
3262626
2000
123
True Positives
IMPA_SALTY    LEXA_AERHY    LEXA_BACSU    LEXA_ECOLI    
LEXA_ERWCA LEXA_HAEIN LEXA_PRORE LEXA_PSEAE
LEXA_PSEPU LEXA_SALTY MUCA_SALTY O32506
O33927 O52206 O52210 O69979
O86050 O86847 O86948 Q10466
Q44053 Q49848 Q50765 SAMA_SALTY
UMUD_ECOLI UMUD_SALTY
Sequence Titles
IMPA_SALTY  IMPA PROTEIN (EC 3.4.21.-) [CONTAINS: IMPA' PROTEIN] - SALMONELLA TYPHIMURIUM. 
LEXA_AERHY LEXA REPRESSOR (EC 3.4.21.88) - AEROMONAS HYDROPHILA.
LEXA_BACSU SOS REGULATORY PROTEIN LEXA/DINR - BACILLUS SUBTILIS.
LEXA_ECOLI LEXA REPRESSOR (EC 3.4.21.88) - ESCHERICHIA COLI.
LEXA_ERWCA LEXA REPRESSOR (EC 3.4.21.88) - ERWINIA CAROTOVORA.
LEXA_HAEIN LEXA REPRESSOR (EC 3.4.21.88) - HAEMOPHILUS INFLUENZAE.
LEXA_PRORE LEXA REPRESSOR (EC 3.4.21.88) - PROVIDENCIA RETTGERI.
LEXA_PSEAE LEXA REPRESSOR (EC 3.4.21.88) - PSEUDOMONAS AERUGINOSA.
LEXA_PSEPU LEXA REPRESSOR (EC 3.4.21.88) - PSEUDOMONAS PUTIDA.
LEXA_SALTY LEXA REPRESSOR (EC 3.4.21.88) - SALMONELLA TYPHIMURIUM.
MUCA_SALTY MUCA PROTEIN (EC 3.4.21.-) [CONTAINS: MUCA' PROTEIN] - SALMONELLA TYPHIMURIUM, AND ESCHERICHIA COLI.
O32506 LEXA PROTEIN - DEINOCOCCUS RADIODURANS.
O33927 LEXA - THERMOTOGA MARITIMA.
O52206 MUCA - MORGANELLA MORGANII (PROTEUS MORGANII).
O52210 MUCA - SERRATIA MARCESCENS.
O69979 SOS REGULATORY PROTEIN LEXA - STREPTOMYCES COELICOLOR.
O86050 LEXA - XANTHOMONAS CAMPESTRIS (PV. CITRI).
O86847 LEXA PROTEIN - STREPTOMYCES CLAVULIGERUS.
O86948 LEXA REPRESSOR (EC 3.4.21.88) (REPRESSOR LEXA) - THERMOTOGA NEAPOLITANA.
Q10466 TITIN, HEART ISOFORM N2-B (EC 2.7.1.-) (CONNECTIN) - HOMO SAPIENS (HUMAN).
Q44053 RUMA - PROVIDENCIA RETTGERI.
Q49848 LEXA - MYCOBACTERIUM LEPRAE.
Q50765 LEXA GENE - MYCOBACTERIUM TUBERCULOSIS.
SAMA_SALTY SAMA PROTEIN (EC 3.4.21.-) [CONTAINS: SAMA' PROTEIN] - SALMONELLA TYPHIMURIUM.
UMUD_ECOLI UMUD PROTEIN (EC 3.4.21.-) [CONTAINS: UMUD' PROTEIN] - ESCHERICHIA COLI.
UMUD_SALTY UMUD PROTEIN (EC 3.4.21.-) [CONTAINS: UMUD' PROTEIN] - SALMONELLA TYPHIMURIUM.
Scan History
OWL29_3    2  500  NSINGLE    
SPTR37_9f 3 200 NSINGLE
Initial Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
FLLRVSGMSMK LEXA_ECOLI 111 111 -
FLLRVSGMSMK LEXA_ERWCA 111 111 -
FLLRVNGMSMK LEXA_PRORE 114 114 -
YLLRVHGMSMK LEXA_PSEPU 115 115 -
YFVKASGDSMI UMUD_ECOLI 52 52 -
YFLRVSGSSME MUCA_SALTY 54 54 -
FFLRASGESMN IMPA_SALTY 56 56 -
FMLEIMGDSMI LEXA_BACSU 119 119 -

Motif 2 width=12
Element Seqn Id St Int Rpt
DIGIMDGDLLAV LEXA_ECOLI 122 0 -
NIGIMDGDLLAV LEXA_ERWCA 122 0 -
DIGIMDGDLLAV LEXA_PRORE 125 0 -
DVGIFDGDLLAV LEXA_PSEPU 126 0 -
DGGISDGDLLIV UMUD_ECOLI 63 0 -
DGRIHDGDVLVV MUCA_SALTY 65 0 -
QAGVQNGDLLVV IMPA_SALTY 67 0 -
DAGILDKDYVIV LEXA_BACSU 130 0 -

Motif 3 width=13
Element Seqn Id St Int Rpt
DDEVTVKRLKKQG LEXA_ECOLI 150 16 -
DDEVTVKRLKKQG LEXA_ERWCA 150 16 -
EDEVTVKRFKQQG LEXA_PRORE 153 16 -
GDEVTVKRFKREG LEXA_PSEPU 154 16 -
DGEFTVKKLQLRP UMUD_ECOLI 91 16 -
HNEFTVKRLLLRP MUCA_SALTY 93 16 -
DGEFTVKRLLLRP IMPA_SALTY 95 16 -
DDEATVKRFYKED LEXA_BACSU 159 17 -
Final Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
FLLRVSGMSMK LEXA_ECOLI 111 111 -
FLLRVSGMSMK LEXA_SALTY 111 111 -
FLLRVSGMSMK LEXA_ERWCA 111 111 -
FLLRVNGMSMK LEXA_PRORE 114 114 -
YLLRVRGMSMK LEXA_PSEAE 117 117 -
YLLRVHGMSMK LEXA_PSEPU 115 115 -
FLLRVQGMSMK LEXA_AERHY 116 116 -
FLLKVYGLSMK LEXA_HAEIN 115 115 -
FLLKVIGDSMV Q50765 133 133 -
YFLRVSGDSMR O52210 54 54 -
YFLRVSGDSMR O52206 54 54 -
FLLKVTGDSMV Q49848 151 151 -
YFVKASGDSMI UMUD_SALTY 52 52 -
FVLKVVGDSMI O69979 150 150 -
FVLKVVGDSMI O86847 180 180 -
YFVKASGDSMI UMUD_ECOLI 52 52 -
FLLKVKGESMI O33927 111 111 -
YFLRVSGSSME MUCA_SALTY 54 54 -
FFLRASGESMN IMPA_SALTY 56 56 -
FFVRAIGDSMK SAMA_SALTY 53 53 -
FFVRVEGDSMI Q44053 59 59 -
FLLRVKGESMI O86948 111 111 -
YLLKVQGDSMR O86050 125 125 -
FMLEIMGDSMI LEXA_BACSU 119 119 -
FLLRVRGESMT O32506 112 112 -
FDLKVVGRPMP Q10466 1430 1430 -

Motif 2 width=12
Element Seqn Id St Int Rpt
DIGIMDGDLLAV LEXA_ECOLI 122 0 -
DIGIMDGDLLAV LEXA_SALTY 122 0 -
NIGIMDGDLLAV LEXA_ERWCA 122 0 -
DIGIMDGDLLAV LEXA_PRORE 125 0 -
DIGILDGDLLAV LEXA_PSEAE 128 0 -
DVGIFDGDLLAV LEXA_PSEPU 126 0 -
NIGILDGDLLAV LEXA_AERHY 127 0 -
NVGILDGDLLAV LEXA_HAEIN 126 0 -
EAAICDGDWVVV Q50765 144 0 -
DARIHDGDVLVV O52210 65 0 -
DARIHDGDVLVV O52206 65 0 -
EAAICDGDWVVV Q49848 162 0 -
EAGISDGDLLVV UMUD_SALTY 63 0 -
EAAICDGDWVTV O69979 161 0 -
EAAICDGDWVTV O86847 191 0 -
DGGISDGDLLIV UMUD_ECOLI 63 0 -
EEHICDGDLVLV O33927 122 0 -
DGRIHDGDVLVV MUCA_SALTY 65 0 -
QAGVQNGDLLVV IMPA_SALTY 67 0 -
EMGLHSGDLMVV SAMA_SALTY 64 0 -
DAGIHPDDILVV Q44053 70 0 -
EEHICDGDLVLI O86948 122 0 -
DEGIFNGDLIGV O86050 136 0 -
DAGILDKDYVIV LEXA_BACSU 130 0 -
GIGVMDGDYVVV O32506 123 0 -
EEGELDKDRVVI Q10466 8644 7203 -

Motif 3 width=13
Element Seqn Id St Int Rpt
DDEVTVKRLKKQG LEXA_ECOLI 150 16 -
DDEVTVKRLKKQG LEXA_SALTY 150 16 -
DDEVTVKRLKKQG LEXA_ERWCA 150 16 -
EDEVTVKRFKQQG LEXA_PRORE 153 16 -
GEEVTVKRFKREG LEXA_PSEAE 156 16 -
GDEVTVKRFKREG LEXA_PSEPU 154 16 -
DEDVTVKRFQRKG LEXA_AERHY 155 16 -
EDEVTVKRLEKKG LEXA_HAEIN 154 16 -
DGEATVKTFKRAG Q50765 172 16 -
DNEFTVKQLQLRP O52210 93 16 -
DNEFTVKQLQLRP O52206 93 16 -
DGEATVKTFKRAG Q49848 190 16 -
EGEFTVKRLQLRP UMUD_SALTY 91 16 -
DGEATVKRFKRED O69979 189 16 -
DGEATVKRFKREN O86847 219 16 -
DGEFTVKKLQLRP UMUD_ECOLI 91 16 -
DGEVTLKKFYQRG O33927 150 16 -
HNEFTVKRLLLRP MUCA_SALTY 93 16 -
DGEFTVKRLLLRP IMPA_SALTY 95 16 -
DGEFTVKRLQLKP SAMA_SALTY 92 16 -
HGELTVKELQLRP Q44053 98 16 -
EGEVTLKKFFQRG O86948 150 16 -
DEEITVKLLKIGK O86050 164 16 -
DDEATVKRFYKED LEXA_BACSU 159 17 -
DNAATLKRLYHFG O32506 153 18 -
TEEVVVKEDLQKP Q10466 11692 3036 -