WORKLIST ENTRIES (1):
HTHCRO View alignment View Structure Cro repressor HTH signature
Type of fingerprint: COMPOUND with 2 elements
Links:
PRINTS; PR00031 HTHREPRESSR; PR00024 HOMEOBOX; PR00025 ANTENNAPEDIA
PRINTS; PR00026 ENGRAILED; PR00027 PAIREDBOX; PR00028 POUDOMAIN
PRINTS; PR00029 OCTAMER
INTERPRO; IPR000655
PFAM; PF01381 HTH_3
PDB; 1CRO 3Dinfo
SCOP; 1CRO
CATH; 2CRO
Creation date 23-MAR-1993; UPDATE 10-JUN-1999
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).
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 FINGERPRINT INDEX
2| 2 2
--+-----------
| 1 2
True positives..
RCRO_BP434 RCRO_LAMBD
PROTEIN 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 MOTIF SETS
HTHCRO1 Length of motif = 10 Motif number = 1
Cro repressor HTH motif I - 1
PCODE ST INT
GQTKTAKDLG RCRO_LAMBD 14 14
GQTKTAKDLG NRL_1CROA 14 14
TQTELATKAG NRL_2CRO 17 17
TQTELATKAG NRL_3CROL 17 17
HTHCRO2 Length of motif = 16 Motif number = 2
Cro repressor HTH motif II - 1
PCODE ST INT
GVYQSAINKAIHAGRK RCRO_LAMBD 23 -1
GVYQSAINKAIHAGRK NRL_1CROA 23 -1
GVKQQSIQLIEAGVTK NRL_2CRO 26 -1
GVKQQSIQLIEAGVTK NRL_3CROL 26 -1
FINAL MOTIF SETS
HTHCRO1 Length of motif = 10 Motif number = 1
Cro repressor HTH motif I - 2
PCODE ST INT
TQTELATKAG RCRO_BP434 18 18
GQTKTAKDLG RCRO_LAMBD 15 15
HTHCRO2 Length of motif = 16 Motif number = 2
Cro repressor HTH motif II - 2
PCODE ST INT
GVKQQSIQLIEAGVTK RCRO_BP434 27 -1
GVYQSAINKAIHAGRK RCRO_LAMBD 24 -1
User query: Display/Full Code "HTHCRO"