WORKLIST ENTRIES (1):

PYOCIN View alignment View Structure          Colicin E2 (pyocin) immunity protein signature
 Type of fingerprint: COMPOUND with 3  elements
Links:
   PRINTS; PR01295 CLOACIN; PR01296 CLOACNIMMNTY; PR01297 LYSISCOLICIN
   PRINTS; PR01298 MICROCIN; PR01300 PYOCINKILLER
   PDB; 1IMQ 3Dinfo; 1IMP 3Dinfo
   SCOP; 1IMQ; 1IMP
   CATH; 1IMQ; 1IMP

 Creation date 17-FEB-2000

   1. COLE, S.T., SAINT-JOANIS, B. AND PUGSLEY, A.P.
   Molecular characterisation of the colicin E2 operon and identification
   of its products.
   MOL.GEN.GENET. 198 465-472 (1985). 

   2. WALEH, N.S. AND JOHNSON, P.H.
   Structural and functional organization of the colicin E1 operon.
   PROC.NATL.ACAD.SCI.U.S.A. 82 8389-8393 (1985). 

   3. VAN DEN ELZEN, P.J., GAASTRA, W., SPELT, C.E., DE GRAAF, F.K., VELTKAMP,
   E. AND NIJKAMP, H.J.
   Molecular structure of the immunity gene and immunity protein of the
   bacteriocinogenic plasmid Clo DF13.
   NUCLEIC ACIDS RES. 8 4349-4363 (1980). 
  
   4. OSBORNE, M.J., BREEZE, A.L., LIAN, L.Y., REILLY, A., JAMES, R.,
   KLEANTHOUS, C. AND MOORE, G.R.
   Three-dimensional solution structure and 13C nuclear magnetic resonance
   assignments of the colicin E9 immunity protein Im9.
   BIOCHEMISTRY 35 9505-9512 (1996). 

   The DNA sequence of the entire colicin E2 operon has been determined [1].
   The operon comprises the colicin activity gene (ceaB), the colicin immunity
   gene (ceiB) and the lysis gene (celB), which is essential for colicin
   release from producing cells [1]. A putative LexA binding site is located
   upstream from ceaB, and a rho-independent terminator structure is located
   downstream from celB [1]. Comparison of the amino acid sequences of colicin
   E2 and cloacin DF13 reveal extensive similarity. These colicins have
   different modes of action and recognise different cell surface receptors;
   the two major regions of heterology at the C-terminus, and in the C-terminal
   end of the central region are thought to correspond to the catalytic and 
   receptor-recognition domains, respectively [1]. 
  
   Sequence similarities between colicins E2, A and E1 [2] are less striking.
   The colicin E2 (pyocin) immunity protein does not share similarity with
   either the colicin E3 or cloacin DF13 [3] immunity proteins. Pyocin protects
   a cell that harbours the plasmid ColE2 encoding colicin E2 against colicin 
   E2; it is thus essential both for autonomous replication and colicin E2
   immunity [1]. 
  
   The three-dimensional structure of the colicin E9 immunity protein Im9 has
   been solved by NMR [4]. The fold is a distorted anti-parallel four-helix
   bundle, in which the third helix is rather short, a structure consistent 
   with available kinetic and biochemical data concerning the interaction 
   between Im9 and its target DNase [4]. Important residues that govern
   specificity are located on the molecular surface in a region rich in
   negatively charged groups, consistent with the proposed electrostatically-
   steered association [4]. 
  
   PYOCIN is a 3-element fingerprint that provides a signature for pyocins.
   The fingerprint was derived from an initial alignment of 6 sequences: the
   motifs were drawn from conserved regions spanning the full alignment length
   - motif 1 includes helix 1; motif 2 spans the C-terminus of helix 2 and
   helix 3; and motif 3 includes helix 4. Two iterations on SPTR37_10f were
   required to reach convergence, at which point a true set comprising 9
   sequences was identified.

  SUMMARY INFORMATION
      9 codes involving  3 elements
      0 codes involving  2 elements

   COMPOSITE FINGERPRINT INDEX
  
    3|   9    9    9  
    2|   0    0    0  
   --+----------------
     |   1    2    3  

True positives..
 IMM2_ECOLI     IMM2_PSEAE     IMM1_PSEAE     IMM7_ECOLI     
 IMM9_ECOLI     IMM8_ECOLI     Q57086         IMMX_ECOLI     
 Q51503         


  PROTEIN TITLES
   IMM2_ECOLI       COLICIN E2 IMMUNITY PROTEIN (IMME2) (MICROCIN E2 IMMUNITY PR
   IMM2_PSEAE       IMMUNITY PROTEIN FOR PYOCIN S2 - PSEUDOMONAS AERUGINOSA.
   IMM1_PSEAE       IMMUNITY PROTEIN FOR PYOCIN S1 - PSEUDOMONAS AERUGINOSA.
   IMM7_ECOLI       COLICIN E7 IMMUNITY PROTEIN (IMME7) (MICROCIN E7 IMMUNITY PR
   IMM9_ECOLI       COLICIN E9 IMMUNITY PROTEIN (IMME9) (MICROCIN E9 IMMUNITY PR
   IMM8_ECOLI       COLICIN E8 IMMUNITY PROTEIN (IMME8) (MICROCIN E8 IMMUNITY PR
   Q57086           IMMUNITY PROTEIN 8 - SHIGELLA SONNEI, AND UNIDENTIFIED.
   IMMX_ECOLI       COLICIN E8 IMMUNITY PROTEIN IN COLE6 (E8IMM[E6]) - ESCHERICH
   Q51503           THE SMALL COMPONENT OF PYOCIN AP41 - PSEUDOMONAS AERUGINOSA.

SCAN HISTORY SPTR37_10f 1 100 NSINGLE INITIAL MOTIF SETS PYOCIN1 Length of motif = 19 Motif number = 1 Pyocin motif I - 1 PCODE ST INT KSKISEYTEKEFLEFVEDI IMM1_PSEAE 2 2 KHSISDYTEAEFLEFVKKI IMM2_ECOLI 4 4 KNSISDYTEAEFVQLLKEI IMM7_ECOLI 4 4 KNSISDYTETEFKKIIEDI IMM8_ECOLI 4 4 KHSISDYTEAEFLQLVTTI IMM9_ECOLI 4 4 KSKISEYTEKEFLEFVKDI IMM2_PSEAE 2 2 PYOCIN2 Length of motif = 17 Motif number = 2 Pyocin motif II - 1 PCODE ST INT FKKLTEHPSGSDLLYYP IMM1_PSEAE 41 20 FERLTEHPDGSDLIYYP IMM2_ECOLI 40 17 FVKITEHPDGTDLIYYP IMM7_ECOLI 41 18 FISVTEHPSGSDLIYYP IMM8_ECOLI 39 16 FEEMTEHPSGSDLIYYP IMM9_ECOLI 40 17 FKKLTEHPSGSDLLYYP IMM2_PSEAE 41 20 PYOCIN3 Length of motif = 22 Motif number = 3 Pyocin motif III - 1 PCODE ST INT SPAGVVKEVKEWRASKGLPGFK IMM1_PSEAE 64 6 SPEGIVKEIKEWRAANGKSGFK IMM2_ECOLI 63 6 SPEGIVKEIKEWRAANGKPGFK IMM7_ECOLI 64 6 SPEAVIKEIKEWRAANGKSGFK IMM8_ECOLI 62 6 SPSGIVNTVKQWRAANGKSGFK IMM9_ECOLI 63 6 SPAGVVKEVKEWRASKGLPGFK IMM2_PSEAE 64 6 FINAL MOTIF SETS PYOCIN1 Length of motif = 19 Motif number = 1 Pyocin motif I - 2 PCODE ST INT KHSISDYTEAEFLEFVKKI IMM2_ECOLI 4 4 KSKISEYTEKEFLEFVKDI IMM2_PSEAE 2 2 KSKISEYTEKEFLEFVEDI IMM1_PSEAE 2 2 KNSISDYTEAEFVQLLKEI IMM7_ECOLI 4 4 KHSISDYTEAEFLQLVTTI IMM9_ECOLI 4 4 KNSISDYTETEFKKIIEDI IMM8_ECOLI 4 4 KKSIGDYTETEFKKFIEDI Q57086 4 4 KKSIGDYTETEFKKIIENI IMMX_ECOLI 4 4 KNNLSDYTESEFLEIIEEF Q51503 4 4 PYOCIN2 Length of motif = 17 Motif number = 2 Pyocin motif II - 2 PCODE ST INT FERLTEHPDGSDLIYYP IMM2_ECOLI 40 17 FKKLTEHPSGSDLLYYP IMM2_PSEAE 41 20 FKKLTEHPSGSDLLYYP IMM1_PSEAE 41 20 FVKITEHPDGTDLIYYP IMM7_ECOLI 41 18 FEEMTEHPSGSDLIYYP IMM9_ECOLI 40 17 FISVTEHPSGSDLIYYP IMM8_ECOLI 39 16 FINVTEHPSGSDLIYYP Q57086 39 16 FISVTEHPSGSDLIYYP IMMX_ECOLI 39 16 FEEVTSHPRKSGVIFHP Q51503 45 22 PYOCIN3 Length of motif = 22 Motif number = 3 Pyocin motif III - 2 PCODE ST INT SPEGIVKEIKEWRAANGKSGFK IMM2_ECOLI 63 6 SPAGVVKEVKEWRASKGLPGFK IMM2_PSEAE 64 6 SPAGVVKEVKEWRASKGLPGFK IMM1_PSEAE 64 6 SPEGIVKEIKEWRAANGKPGFK IMM7_ECOLI 64 6 SPSGIVNTVKQWRAANGKSGFK IMM9_ECOLI 63 6 SPEAVIKEIKEWRAANGKSGFK IMM8_ECOLI 62 6 SPEGVIKEIKEWRAANGKSGFK Q57086 62 6 SPEAVIKEIKEWRAANGKSGFK IMMX_ECOLI 62 6 TPEGIVKEVKEWRAANGLPGFK Q51503 67 5

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