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 . 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 . The first helix helps to stabilise the structure . This motif is very similar in sequence and structure to the N-terminal region of the lamda  and other repressor proteins, and has also been identified in many other DNA-binding proteins on the basis of sequence and structure similarity . 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"