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PR00687

Identifier
TRPRNAAP  [View Relations]  [View Alignment]  
Accession
PR00687
No. of Motifs
4
Creation Date
04-APR-1997  (UPDATE 07-JUN-1999)
Title
Tryptophan RNA-binding attenuator protein signature
Database References

INTERPRO; IPR000824
PDB; 1WAP
SCOP; 1WAP
CATH; 1WAP
Literature References
1. GOLLNICK, P., ISHINO, S., KURODA, M.I., HENNER, D.J. AND YANOFSKY, C.
The mtr locus is a two-gene operon required for transcription attenuation
in the trp operon of Bacillus subtilis.  
PROC.NATL.ACAD.SCI.U.S.A. 87(22) 8726-8730 (1990).
 
2. BABITZKE, P., GOLLNICK, P. AND YANOFSKY, C.
The mtrAB operon of Bacillus subtilis encodes GTP cyclohydrolase I (mtrA), 
an enzyme involved in folic acid biosynthesis, and mtrB, a regulator of 
tryptophan biosynthesis.
J.BACTERIOL. 174(7) 2059-2064 (1992). 
 
3. ANTSON, A.A., BRZOZOWSKI, A.M., DODSON, E.J., DAUTER, Z., WILSON, K.S.,
KURECKI, T., OTRIDGE, J. AND GOLLNICK, P.
11-fold symmetry of the Trp RNA-binding attenuation protein (TRAP) from
Bacillus subtilis determined by X-ray analysis.
J.MOL.BIOL. 18 244(1) 1-5 (1994).
 
4. ANTSON, A.A., OTRIDGE, J., BRZOZOWSKI, A.M., DODSON, E.J., DODSON, G.G.,
WILSON, K.S., SMITH, T.M., YANG, M., KURECKI, T. AND GOLLNICK, P.
The structure of Trp RNA-binding attenuation protein.
NATURE 374 693-700 (1995).

Documentation
The mtr operon encodes a presumed RNA-binding regulatory protein that is
required for attenuation control of the trp operon [1]. The operon consists
of two structural genes, mtrA and mtrB, predicted to encode 22kDa and 6kDa
polypeptides respectively [1,2]. MtrB is similar to RegA, an RNA-binding
regulatory protein of bacteriophage T4. Both mtrA and mtrB have been shown
to be necessary for regulation of beta-galactosidase production. 
 
The crystal structure of the Trp RNA-binding attenuation protein of 
B.subtilis has been solved [3,4]. The protein is an ondecamer of 7-stranded 
beta-sandwiches. The 11 subunits are stabilised by 11 inter-subunit strands,
forming a beta-wheel with a large central hole. The binding of L-tryptophan
in clefts between adjacent strands induces conformational changes in the
protein [4]. It is possible that, on binding, the mRNA target forms a
matching circle in which 11 U/GAG repeats are bound to the surface of the
protein ondecamer modified by the binding of L-tryptophan [4]. 
 
TRPRNAAP is a 4-element fingerprint that provides a signature for the
transcription attenuation protein mtrB. The fingerprint was derived from
an initial alignment of 2 sequences: the motifs span the full alignment
length - motif 1 spans strands 1 and 2; motif 2 includes strand 3; motif 3
spans strands 4 and 5; and motif 4 spans strands 6 and 7. A single iteration 
on OWL29.2 was required to reach convergence, no further sequences being
identified beyond the starting set.
 
An update on SPTR37_9f identified a true set of 2 sequences.
Summary Information
2 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
42222
30000
20000
1234
True Positives
MTRB_BACPU    MTRB_BACSU    
Sequence Titles
MTRB_BACPU  TRANSCRIPTION ATTENUATION PROTEIN MTRB (TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN) (TRAP) - BACILLUS PUMILUS. 
MTRB_BACSU TRANSCRIPTION ATTENUATION PROTEIN MTRB (TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN) (TRAP) - BACILLUS SUBTILIS.
Scan History
OWL29_2    1  50   NSINGLE    
SPTR37_9f 2 4 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
FVVIKAIDNGVNVIGLTR MTRB_BACPU 9 9 -
FVVIKAVEDGVNVIGLTR MTRB_BACSU 9 9 -

Motif 2 width=17
Element Seqn Id St Int Rpt
RGSDTRFHHSEKLDKGE MTRB_BACPU 26 -1 -
RGTDTKFHHSEKLDKGE MTRB_BACSU 26 -1 -

Motif 3 width=17
Element Seqn Id St Int Rpt
EVIIAQFTEHTSAIKVR MTRB_BACPU 42 -1 -
EVIIAQFTEHTSAIKVR MTRB_BACSU 42 -1 -

Motif 4 width=17
Element Seqn Id St Int Rpt
RGDAVIQTSFGEIQSEA MTRB_BACPU 58 -1 -
RGEALIQTAYGEMKSEK MTRB_BACSU 58 -1 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
FVVIKAIDNGVNVIGLTR MTRB_BACPU 9 9 -
FVVIKAVEDGVNVIGLTR MTRB_BACSU 9 9 -

Motif 2 width=17
Element Seqn Id St Int Rpt
RGSDTRFHHSEKLDKGE MTRB_BACPU 26 -1 -
RGTDTKFHHSEKLDKGE MTRB_BACSU 26 -1 -

Motif 3 width=17
Element Seqn Id St Int Rpt
EVIIAQFTEHTSAIKVR MTRB_BACPU 42 -1 -
EVIIAQFTEHTSAIKVR MTRB_BACSU 42 -1 -

Motif 4 width=17
Element Seqn Id St Int Rpt
RGDAVIQTSFGEIQSEA MTRB_BACPU 58 -1 -
RGEALIQTAYGEMKSEK MTRB_BACSU 58 -1 -