Summary: Helix-hairpin-helix motif
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Helix-hairpin-helix motif Provide feedback
Doherty AJ, Serpell LC, Ponting CP; , Nucleic Acids Res 1996;24:2488-2497.: The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. PUBMED:8692686 EPMC:8692686
Rafferty JB, Sedelnikova SE, Hargreaves D, Artymiuk PJ, Baker PJ, Sharples GJ, Mahdi AA, Lloyd RG, Rice DW; , Science 1996;274:415-421.: Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction. PUBMED:8832889 EPMC:8832889
Witte G, Hartung S, Buttner K, Hopfner KP; , Mol Cell. 2008;30:167-178.: Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. PUBMED:18439896 EPMC:18439896
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000445The HhH motif is a stretch of approximately 20 amino acids that is present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [PUBMED:7664751, PUBMED:9973609, PUBMED:9987128]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix [PUBMED:7664751]. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups [PUBMED:8692686]. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins and binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity [PUBMED:8692686].
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|Molecular function||DNA binding (GO:0003677)|
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Curation and family details
|Number in seed:||104|
|Number in full:||8740|
|Average length of the domain:||29.70 aa|
|Average identity of full alignment:||42 %|
|Average coverage of the sequence by the domain:||10.45 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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There are 4 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the HHH domain has been found. There are 41 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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