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PR01591

Identifier
DNABINDNGFIS  [View Relations]  [View Alignment]  
Accession
PR01591
No. of Motifs
4
Creation Date
22-SEP-2001
Title
DNA-binding protein FIS signature 
Database References
PRINTS; PR01590 HTHFIS
PDB; 1ETY
SCOP; 1ETY
CATH; 1ETY
Literature References
1. OSUNA, R., LIENAU, D., HUGHES, K.T. AND JOHNSON, R.C.
Sequence, regulation, and function of fis in Salmonella typhimurium.
J.BACTERIOL. 177 2021-2032 (1995).
 
2. WILSON, R.L., LIBBY, S.J., FREET, A.M., BODDICKER, J.D., FAHLEN, T.F.
AND JONES, B.D.
Fis, a DNA nucleoid-associated protein, is involved in Salmonella 
typhimurium SPI-I invasion gene expression.
MOL.MICROBIOL. 39 79-88 (2001).
 
3. GOLDBERG, M.D., JOHNSON, M., HINTON, J.C. AND WILLIAMS, P.H.
Role of the nucleoid-associated protein Fis in the regulation of virulence 
properties of enteropathogenic Escherichia coli.
MOL.MICROBIOL. 41 549-559 (2001).
 
4. MORETT, E. AND BORK, P.
Evolution of new protein function: recombinational enhancer Fis originated 
by horizontal gene transfer from the transcriptional regulator NtrC.
FEBS LETT. 433 108-112 (1998).
 
5. CHENG, Y.S., YANG, W.Z., JOHNSON, R.C. AND YUAN, H.S.
Structural analysis of the transcriptional activation on Fis: crystal 
structures of six Fis mutants with different activation properties.
J.MOL.BIOL. 302 1139-1151 (2000).
 
6. YUAN, H.S., FINKEL, S.E., FENG, J-A., KACZOR-GRZESKOWIAK, M.,
JOHNSON., R.C. AND DICKERSON, R.E.
The molecular structure of wild-type and a mutant Fis protein: Relationship 
between mutational changes and recombinational enhancer function or DNA 
binding.
PROC.NATL.ACAD.SCI.U.S.A. 88 9558-9562 (1991).

Documentation
Transcriptional regulators of prokaryotes play an important role in the 
production of several proteins, and in the growth of the cell [1]. By 
regulating gene expression, activation or repression of transcription of a 
variety of genes can be achieved [1]. 
 
The Factor for Inversion Stimulation (FIS) protein is a regulator of
bacterial functions, and binds specifically to weakly related DNA sequences 
[1,2]. It activates ribosomal RNA transcription, and is involved in upstream
activation of rRNA promoters. Found in gamma proteobacterial microbes, the
protein has been shown to play a part in the regulation of virulence factors
in both Salmonella typhimurium and Esherichia coli [2,3]. Some of its
functions include inhibition of the initiation of DNA replication from the
OriC site, and promotion of Hin-mediated DNA inversion [3].
 
In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA-
binding motif, which shares a high degree of similarity with other HTH
motifs of more primitive bacterial transcriptional regulators, such as the
nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter,
Rhodobacter and Rhizobium. This has led to speculation that both evolved
from a single common ancestor [4]. 
 
Recently, the crystal structure of wild-type Escherichia coli FIS was 
resolved, together with six mutants [5] - the first crystal structure was
solved in 1991 [6]. From the most recent 2.0A structure [6] of wild-type
FIS, the protein was observed to exist as a homodimer in the bacterial
cytoplasm. By comparison with the structures of FIS mutants, it was deduced
that arginine-71 is critical for the binding of FIS to RNA polymerase, while
glycine-72 stabilises the tertiary structure [6].
 
DNABINDNGFIS is a 4-element fingerprint that provides a signature for the 
DNA-binding protein FIS. The fingerprint was derived from an initial 
alignment of 7 sequences: the motifs were drawn from conserved regions 
spanning the N-terminal portion of the alignment, prior to the HTH motif -
motif 2 encodes alpha helix 1; and motifs 3 and 4 span helix 2. A single
iteration on SPTR39.22_17.3f was required to reach convergence, no further
sequences being identified beyond the starting set. Two partial matches were
found, both of which are DNA-binding proteins that fail to make significant
matches with one or more motifs.
Summary Information
   7 codes involving  4 elements
1 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
47777
30111
20110
1234
True Positives
FIS_BUCAI     FIS_ECOLI     FIS_ERWCA     FIS_HAEIN     
FIS_PASHA FIS_PASMU Q9KV67
True Positive Partials
Codes involving 3 elements
Q9HUW0
Codes involving 2 elements
Q9PBY7
Sequence Titles
FIS_BUCAI   DNA-BINDING PROTEIN FIS - Buchnera aphidicola (subsp. Acyrthosiphon pisum) (Acyrthosiphon pisum symbiotic bacterium). 
FIS_ECOLI DNA-BINDING PROTEIN FIS (FACTOR-FOR-INVERSION STIMULATION PROTEIN) (HIN RECOMBINATIONAL ENHANCER BINDING PROTEIN) - Escherichia coli, and Salmonella typhimurium.
FIS_ERWCA DNA-BINDING PROTEIN FIS - Erwinia carotovora.
FIS_HAEIN DNA-BINDING PROTEIN FIS - Haemophilus influenzae.
FIS_PASHA DNA-BINDING PROTEIN FIS - Pasteurella haemolytica.
FIS_PASMU DNA-BINDING PROTEIN FIS - Pasteurella multocida.
Q9KV67 FACTOR-FOR-INVERSION STIMULATION PROTEIN - Vibrio cholerae.

Q9HUW0 DNA-BINDING PROTEIN FIS - Pseudomonas aeruginosa.

Q9PBY7 DNA-BINDING PROTEIN - Xylella fastidiosa.
Scan History
SPTR39.22_17.3f 1  80   NSINGLE    
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
DVLTVSTVNSQDQVTQKP FIS_ECOLI 9 9 -
DVLTVSTVNSQAQVTQKP FIS_ERWCA 9 9 -
DALTVSVLNSQSQVTNKP FIS_PASMU 10 10 -
DALTVSVLNAQSQVTSKP FIS_HAEIN 10 10 -
EALTVTTVTSQDQITQKP Q9KV67 9 9 -
NPLTVTMLNAQAQQVNKP FIS_PASHA 9 9 -
EFLVLSTTNTQDKNIKQP FIS_BUCAI 9 9 -

Motif 2 width=17
Element Seqn Id St Int Rpt
PLRDSVKQALKNYFAQL FIS_ECOLI 26 -1 -
PLRDSVKQALKNYFAQL FIS_ERWCA 26 -1 -
PLRDSVKQALRNYLSQL FIS_PASMU 27 -1 -
PLRDSVKQALRNYLAQL FIS_HAEIN 27 -1 -
PLRDSVKASLKNYLAQL Q9KV67 26 -1 -
PLRDNVKAALKNYLSQL FIS_PASHA 26 -1 -
PLCELVKKSLKYYLSNL FIS_BUCAI 26 -1 -

Motif 3 width=16
Element Seqn Id St Int Rpt
LNGQDVNDLYELVLAE FIS_ECOLI 42 -1 -
LNGQDVSDLYELVLAE FIS_ERWCA 42 -1 -
LDGQDVNELYELVLAE FIS_PASMU 43 -1 -
LDGQDVNDLYELVLAE FIS_HAEIN 43 -1 -
LNGQEVTELYELVLAE Q9KV67 42 -1 -
LNGEDPTELYELVLSE FIS_PASHA 42 -1 -
LNGKDVNNLYELALSE FIS_BUCAI 42 -1 -

Motif 4 width=13
Element Seqn Id St Int Rpt
EVEQPLLDMVMQY FIS_ECOLI 57 -1 -
EVEQPLLDMVMQY FIS_ERWCA 57 -1 -
EVEHPMLDMVMQY FIS_PASMU 58 -1 -
EVEHPMLDMIMQY FIS_HAEIN 58 -1 -
EVEQPLLDTIMQY Q9KV67 57 -1 -
EIEHPMLDMVMQY FIS_PASHA 57 -1 -
ELEQPLLDMIMQY FIS_BUCAI 57 -1 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
DVLTVSTVNSQDQVTQKP FIS_ECOLI 9 9 -
DVLTVSTVNSQAQVTQKP FIS_ERWCA 9 9 -
DALTVSVLNSQSQVTNKP FIS_PASMU 10 10 -
DALTVSVLNAQSQVTSKP FIS_HAEIN 10 10 -
EALTVTTVTSQDQITQKP Q9KV67 9 9 -
NPLTVTMLNAQAQQVNKP FIS_PASHA 9 9 -
EFLVLSTTNTQDKNIKQP FIS_BUCAI 9 9 -

Motif 2 width=17
Element Seqn Id St Int Rpt
PLRDSVKQALKNYFAQL FIS_ECOLI 26 -1 -
PLRDSVKQALKNYFAQL FIS_ERWCA 26 -1 -
PLRDSVKQALRNYLSQL FIS_PASMU 27 -1 -
PLRDSVKQALRNYLAQL FIS_HAEIN 27 -1 -
PLRDSVKASLKNYLAQL Q9KV67 26 -1 -
PLRDNVKAALKNYLSQL FIS_PASHA 26 -1 -
PLCELVKKSLKYYLSNL FIS_BUCAI 26 -1 -

Motif 3 width=16
Element Seqn Id St Int Rpt
LNGQDVNDLYELVLAE FIS_ECOLI 42 -1 -
LNGQDVSDLYELVLAE FIS_ERWCA 42 -1 -
LDGQDVNELYELVLAE FIS_PASMU 43 -1 -
LDGQDVNDLYELVLAE FIS_HAEIN 43 -1 -
LNGQEVTELYELVLAE Q9KV67 42 -1 -
LNGEDPTELYELVLSE FIS_PASHA 42 -1 -
LNGKDVNNLYELALSE FIS_BUCAI 42 -1 -

Motif 4 width=13
Element Seqn Id St Int Rpt
EVEQPLLDMVMQY FIS_ECOLI 57 -1 -
EVEQPLLDMVMQY FIS_ERWCA 57 -1 -
EVEHPMLDMVMQY FIS_PASMU 58 -1 -
EVEHPMLDMIMQY FIS_HAEIN 58 -1 -
EVEQPLLDTIMQY Q9KV67 57 -1 -
EIEHPMLDMVMQY FIS_PASHA 57 -1 -
ELEQPLLDMIMQY FIS_BUCAI 57 -1 -