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PR00929

Identifier
ATHOOK  [View Relations]  [View Alignment]  
Accession
PR00929
No. of Motifs
3
Creation Date
19-AUG-1998  (UPDATE 13-JUN-1999)
Title
AT-hook-like domain signature
Database References
PRINTS; PR00930 HIGHMOBLTYIY
INTERPRO; IPR000637
PDB; 2EZD; 2EZE; 2EZF; 2EZG
SCOP; 2EZD
CATH; 2EZD
Literature References
1. REEVES, R. AND NISSEN, M.S.
The A.T-DNA-binding domain of mammalian high mobility group-I chromosomal
proteins - a novel peptide motif for recognizing DNA-structure.
J.BIOL.CHEM. 265 8573-8582 (1990).
 
2. FRIEDMANN, M., HOLTH, L.T., ZOGHBI H.Y. AND REEVES, R. 
Organization, inducible-expression and chromosome localization of the human
HMG-I(Y) nonhistone protein gene. 
NUCLEIC ACIDS RES. 21 4259-4267 (1993). 

Documentation
High mobility group (HMG)I proteins bind preferentially to the minor groove
of A.T-rich regions in double-stranded DNA [1,2]. DNA-binding of these, and
several related, proteins is effected by an 11-residue domain known as an
A.T-hook [1].
 
Within known HMG-I proteins are found three highly conserved regions, 
closely related to the consensus sequence TPKRPRGRPKK [1]. A synthetic 
oligopeptide with this sequence specifically binds to substrate DNA in a
manner reminiscent of intact HMG-I proteins. Structure predictions suggest
that the peptide has a secondary structure similar to the anti-tumour and
anti-viral drugs netropsin and distamycin, and to the dye Hoechst 33258 [1]. 
These ligands, which also preferentially bind to A.T-rich DNA, effectively
compete with both the synthetic peptide and the HMG-I proteins for DNA 
binding [1]. The peptide also contains novel structural features such as a
predicted Asx bend, or "hook", at its N-terminus, and laterally-projecting
cationic Arg/Lys "bristles", which may play a role in the binding of HMG-I
proteins [1]. The predicted peptide structure, the A.T-hook, is a previously
undescribed DNA-binding motif [1].
 
ATHOOK is a 3-element fingerprint that provides a signature for AT-hook-like
domains. The fingerprint was derived from an initial alignment of 5
sequences: the motifs were drawn from 3 consecutive hook regions. Two
iterations on OWL30.2 were required to reach convergence, at which point
a true set comprising 20 sequences was identified. Several partial matches
were also found, all of which are DNA-binding proteins with regions of
sequence showing strong similarity to the hook domain. Note that the motifs
in this fingerprint are short and of low complexity. The fingerprint is 
therefore not highly diagnostic, and results should therefore be treated
with a degree of caution.
 
An update on SPTR37_9f identified a true set of 24 sequences, and 2
partial matches.
Summary Information
  24 codes involving  3 elements
2 codes involving 2 elements
Composite Feature Index
3242424
2121
123
True Positives
CPD1_DROME    HMGA_SOYBN    HMGC_HUMAN    HMGC_MOUSE    
HMGI_HUMAN HMGY_HUMAN HMGY_MOUSE O45912
O73816 O88791 P92954 PRH_PETCR
Q22204 Q23793 Q23794 Q38778
Q40451 Q40725 Q42461 Q42492
Q43386 Q43600 Q43877 Q50887
True Positive Partials
Codes involving 2 elements
O80834 SNF2_YEAST
Sequence Titles
CPD1_DROME  CHROMOSOMAL PROTEIN D1 - DROSOPHILA MELANOGASTER (FRUIT FLY). 
HMGA_SOYBN HMG-Y RELATED PROTEIN A (SB16A PROTEIN) - GLYCINE MAX (SOYBEAN).
HMGC_HUMAN HIGH MOBILITY GROUP PROTEIN HMGI-C - HOMO SAPIENS (HUMAN).
HMGC_MOUSE HIGH MOBILITY GROUP PROTEIN HMGI-C - MUS MUSCULUS (MOUSE).
HMGI_HUMAN HIGH MOBILITY GROUP PROTEIN HMG-I - HOMO SAPIENS (HUMAN).
HMGY_HUMAN HIGH MOBILITY GROUP PROTEIN HMG-Y - HOMO SAPIENS (HUMAN).
HMGY_MOUSE HIGH MOBILITY GROUP PROTEIN HMG-Y - MUS MUSCULUS (MOUSE).
O45912 Y17G7A.1 PROTEIN - CAENORHABDITIS ELEGANS.
O73816 HIGH MOBILITY GROUP PROTEIN I-C - GALLUS GALLUS (CHICKEN).
O88791 NON-HISTONE CHROMOSOMAL ARCHITECTURAL PROTEIN HMGI-C - RATTUS NORVEGICUS (RAT).
P92954 HMG-I/Y GENE - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
PRH_PETCR PATHOGENESIS-RELATED HOMEODOMAIN PROTEIN (PRHP) - PETROSELINUM CRISPUM (PARSLEY) (PETROSELINUM HORTENSE).
Q22204 SIMILAR TO AAC-RICH MRNA CLONE AAC11 PROTEIN - CAENORHABDITIS ELEGANS.
Q23793 HIGH MOBILITY GROUP PROTEIN I/Y - CHIRONOMUS TENTANS (MIDGE).
Q23794 HIGH MOBILITY GROUP PROTEIN I/Y - CHIRONOMUS TENTANS (MIDGE).
Q38778 DNA-BINDING PROTEIN - AVENA SATIVA (OAT).
Q40451 DNA-BINDING PROTEIN - NICOTIANA TABACUM (COMMON TOBACCO).
Q40725 AT HOOK-CONTAINING PROTEIN - ORYZA SATIVA (RICE).
Q42461 HIGH MOBILITY GROUP PROTEIN - CANAVALIA GLADIATA (SWORD BEAN) (JAPANESE JACK BEAN).
Q42492 HIGH MOBILITY PROTEIN - CANAVALIA GLADIATA (SWORD BEAN) (JAPANESE JACK BEAN).
Q43386 HMG-I/Y PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
Q43600 POSITIVE ELEMENT FACTOR 1 (PF1) - ORYZA SATIVA (RICE).
Q43877 HMGI/Y - PISUM SATIVUM (GARDEN PEA).
Q50887 CARD GENE AND OPEN READING FRAMES - MYXOCOCCUS XANTHUS.

O80834 PUTATIVE DNA-BINDING PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
SNF2_YEAST TRANSCRIPTION REGULATORY PROTEIN SNF2 (SWI/SNF COMPLEX COMPONENT SNF2) (REGULATORY PROTEIN SWI2) (REGULATORY PROTEIN GAM1) (TRANSCRIPTION FACTOR TYE3) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
Scan History
OWL30_2    2  100  NSINGLE    
SPTR37_9f 3 100 NSINGLE
Initial Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
KRGRGRPRKQQ HMGC_HUMAN 26 26 -
KRGRGRPRKQQ HMGC_MOUSE 26 26 -
KRGRGRPRKQP HMGY_MOUSE 22 22 -
KRGRGRPRKQP HMGY_HUMAN 22 22 -
KRGRGRPRKQP HMGI_HUMAN 22 22 -

Motif 2 width=12
Element Seqn Id St Int Rpt
SPKRPRGRPKGS HMGC_HUMAN 44 7 -
SPKRPRGRPKGS HMGC_MOUSE 44 7 -
TPKRPRGRPKGS HMGY_MOUSE 41 8 -
TPKRPRGRPKGS HMGY_HUMAN 41 8 -
TPKRPRGRPKGS HMGI_HUMAN 52 19 -

Motif 3 width=11
Element Seqn Id St Int Rpt
GEKRPRGRPRK HMGC_HUMAN 72 16 -
GEKRPRGRPRK HMGC_MOUSE 72 16 -
PGRKPRGRPKK HMGY_MOUSE 67 14 -
PGRKPRGRPKK HMGY_HUMAN 67 14 -
PGRKPRGRPKK HMGI_HUMAN 78 14 -
Final Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
KRGRGRPPKPK Q42492 86 86 -
KRGRGRPPKPK Q42461 86 86 -
KRGRGRPPKPK HMGA_SOYBN 84 84 -
KRGRGRPRKQP O73816 26 26 -
KRGRGRPRKQP O88791 26 26 -
KRGRGRPRKQQ HMGC_HUMAN 26 26 -
KRGRGRPRKQQ HMGC_MOUSE 26 26 -
KRGRGRPPKAK Q43877 86 86 -
KRGRGRPPKQK P92954 97 97 -
KRGRGRPPKQK Q43386 97 97 -
KRGRGRPRKQP HMGY_MOUSE 22 22 -
KRGRGRPRKQP HMGY_HUMAN 22 22 -
KRGRGRPRKQP HMGI_HUMAN 22 22 -
KRGRGRPPKPK Q43600 98 98 -
KRGRGRPPKVK Q38778 87 87 -
KRGRGRPRKVQ PRH_PETCR 228 228 -
KPGRGRPRKNP Q40725 135 135 -
KKGRGRPAKAK Q23794 7 7 -
KKGRGRPAKAK Q23793 7 7 -
KKGRGRPIKNP O45912 141 141 -
KRKPGRPPKLK Q40451 139 139 -
GAPRGRPRKSD Q22204 61 61 -
IKKRGRPAKNK CPD1_DROME 33 33 -
PKKRGRPPKAK Q50887 233 233 -

Motif 2 width=12
Element Seqn Id St Int Rpt
SPPRPRGRPPKD Q42492 106 9 -
SPPRPRGRPPKD Q42461 106 9 -
SPPRPRGRPPKD HMGA_SOYBN 104 9 -
SPKRPRGRPKGS O73816 44 7 -
SPKRPRGRPKGS O88791 44 7 -
SPKRPRGRPKGS HMGC_HUMAN 44 7 -
SPKRPRGRPKGS HMGC_MOUSE 44 7 -
STPRPRGRPPKD Q43877 108 11 -
DPPRSRGRPPKP P92954 128 20 -
DPPRSRGRPPKP Q43386 128 20 -
TPKRPRGRPKGS HMGY_MOUSE 41 8 -
TPKRPRGRPKGS HMGY_HUMAN 41 8 -
TPKRPRGRPKGS HMGI_HUMAN 52 19 -
SSPRPRGRPPKP Q43600 127 18 -
SSGRPRGRPAKA Q38778 109 11 -
TGKRSRGRPRKV PRH_PETCR 261 22 -
GVKRGRGRPRKD Q40725 304 158 -
APKKGRGRPSKG Q23794 52 34 -
APKKGRGRPSKG Q23793 52 34 -
PVKKGRGRPAKN O45912 184 32 -
GSKRRPGRPPKS Q40451 307 157 -
SPKRSRGAPKSY Q22204 91 19 -
SPTKGRGRPKSS CPD1_DROME 91 47 -
PAPKKRGRPPKP Q50887 253 9 -

Motif 3 width=11
Element Seqn Id St Int Rpt
GSGRPRGRPKK Q42492 132 14 -
GSGRPRGRPKK Q42461 132 14 -
GSGRPRGRPKK HMGA_SOYBN 130 14 -
GEKRPRGRPRK O73816 72 16 -
GEKRPRGRPRK O88791 72 16 -
GEKRPRGRPRK HMGC_HUMAN 72 16 -
GEKRPRGRPRK HMGC_MOUSE 72 16 -
GSGRPRGRPKK Q43877 131 11 -
GSGRPRGRPPK P92954 153 13 -
GSGRPRGRPPK Q43386 153 13 -
PGRKPRGRPKK HMGY_MOUSE 67 14 -
PGRKPRGRPKK HMGY_HUMAN 67 14 -
PGRKPRGRPKK HMGI_HUMAN 78 14 -
PVKRGRGRPPK Q43600 190 51 -
PAKRGRGRPPK Q38778 151 30 -
AGKRGRGRPRK PRH_PETCR 369 96 -
VGKRGRGRPKK Q40725 406 90 -
ASGKGRGRPAK Q23794 72 8 -
ASGKGRGRPAK Q23793 72 8 -
PVKKGRGRPLK O45912 229 33 -
PLGKRRGRPPK Q40451 439 120 -
GEKKGRGRPKK Q22204 126 23 -
PTGRPRGRPKA CPD1_DROME 216 113 -
PAPKKRGRPPK Q50887 276 11 -