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PR00030

Identifier
HTHCRO  [View Relations]  [View Alignment]  
Accession
PR00030
No. of Motifs
2
Creation Date
23-MAR-1993  (UPDATE 10-JUN-1999)
Title
Cro repressor helix-turn-helix signature
Database References

PFAM; PF01381 HTH_3
INTERPRO; IPR000655
PDB; 1CRO
SCOP; 1CRO
CATH; 2CRO
Literature References
1. TAKEDA, Y., KIM, J.G., CADSAY, C.G., STEERS, E., OHLENDORF, D.H.,
ANDERSON, W.F., AND MATTHEWS, B.W.
Different interactions used by cro repressor in specific and non-specific
DNA-binding.
J.BIOL.CHEM. 261 8608-8616 (1986)
 
2. OHLENDORF, D.H., ANDERSON, W.F., LEWIS, M., PABO, C.O. AND MATTHEWS, B.W.
Comparison of the structures of Cro and Lambda repressor proteins from
Bacteriophage Lambda.
J.MOL.BIOL. 169  757-769 (1983)
 
3. BRENNAN, R.G., TAKEDA, Y., KIM, J., ANDERSON, W.F., AND  MATTHEWS, B.W.
Crystallization of a complex of cro repressor with a 17 base pair operator.
J.MOL.BIOL. 188 115-118 (1986)
 
4. SAUER, R.T.,YOCUM, R.R., DOOLITTLE, R.F., LEWIS, M. AND PABO, C.O.
Homology among DNA-binding proteins suggests use of a conserved super-
secondary structure.
NATURE 298 447-451 (1982)

Documentation
The cro family comprises a set of small, single-domain DNA binding proteins
that regulate phage transcription by binding to DNA in a sequence-specific 
manner using a characteristic helix-turn-helix (HTH) motif [1]. The motif 
occurs between residues 16-35: it consists of 2 alpha-helices joined by a 
short turn that contains a critically conserved glycine (position 9 in
the motif). The second helix binds to DNA via a number of hydrogen bonds 
and hydrophobic interactions, which occur between specific side chains and 
the exposed bases and thymine methyl groups within the major groove of the 
DNA [3]. The first helix helps to stabilise the structure [4]. This motif 
is very similar in sequence and structure to the N-terminal region of the 
lamda [2] and other repressor proteins, and has also been identified in 
many other DNA-binding proteins on the basis of sequence and structure 
similarity [1]. 
 
HTHCRO is a 2-element fingerprint that provides a signature for the HTH
motif of cro repressors. The fingerprint was derived from an initial 
alignment of 4 sequences: the motifs span the complete motif and hinge on
the conserved glycine. Two iterations on OWL19.1 were required to reach
convergence, at which point a true set comprising 15 sequences was
identified. One cro sequence was not found, RCRO_BPP22, which appears
to be more similar to other repressor proteins than to the cro family.
 
An update on SPTR37_9f identified a true set of 2 sequences.
Summary Information
2 codes involving  2 elements
Composite Feature Index
222
12
True Positives
RCRO_BP434    RCRO_LAMBD    
Sequence Titles
RCRO_BP434  REGULATORY PROTEIN CRO - BACTERIOPHAGE 434.   
RCRO_LAMBD REGULATORY PROTEIN CRO - BACTERIOPHAGE LAMBDA.
Scan History
OWL19_1    2  100  NSINGLE    
OWL26_0 1 300 NSINGLE
SPTR37_9f 2 3 NSINGLE
Initial Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
TQTELATKAG N_3CROL 17 17 -
TQTELATKAG N_2CRO 17 17 -
GQTKTAKDLG RCRO_LAMBD 14 14 -
GQTKTAKDLG N_1CROA 14 14 -

Motif 2 width=16
Element Seqn Id St Int Rpt
GVYQSAINKAIHAGRK RCRO_LAMBD 23 -1 -
GVYQSAINKAIHAGRK N_1CROA 23 -1 -
GVKQQSIQLIEAGVTK N_2CRO 26 -1 -
GVKQQSIQLIEAGVTK N_3CROL 26 -1 -
Final Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
TQTELATKAG RCRO_BP434 18 18 -
GQTKTAKDLG RCRO_LAMBD 14 14 -

Motif 2 width=16
Element Seqn Id St Int Rpt
GVKQQSIQLIEAGVTK RCRO_BP434 27 -1 -
GVYQSAINKAIHAGRK RCRO_LAMBD 23 -1 -