... Homeodomain is a DNA-binding domain presented in a number of eukariotic transcription factors that are resposible for regulation of key developmental processes. Homeodomains contain three alpha-helixes forming helix-turn-helix (HTH) topology and a flexible, enriched with basic amino acids N-terminal "hand" (residues 1?9), which changes its conformation during DNA binding. ... Such complexes gain in high specific binding and affinity to DNA. ...
In general, homing endonucleases are meganucleases (i.e. they recognise and cut DNA sequences longer than 12 bp) encoded in various intervening sequences. ... Here we investigate the diversity of yeast intein-encoded LAGLIDADG endonucleases, and annotate their particular residues in terms of importance for DNA recognition, binding and cleavage. PFAM family PF05204 contains sequences of most of the yeast intein-encoded LAGLIDADG endonucleases. ...
Parameters: . Atom list: strict . Model number (for NMR): not applicable to biounits . All chains selected . Distance threshold: 5.4 Input file: 1a1l.pdb1.pdb . Output files: . 1a1l.pdb1.rsc RasMol script . 1a1l.pdb1.txt text table Goto Jmol page . You must run Java enabled browser, compatible with Jmol. More information is available at http://jmol.sourceforge.net/docs/JmolAppletGuide.html#SupportedBrowsers . Ask a question about this service: sas@belozersky.msu.ru
The entry 1QPI contains 1 protein chain: A, and 2 DNA chains: M and N. The length of two DNA chains are identical (15 nucleotide residues), their sequences are similar (differ in 3 positions of 15). ... All atoms of the chain N have alter codes "A", and all atoms of the chain M have alter codes "B". All DNA atoms have occupancy 0.5. ...
The entry 1FJL contains 3 protein chains: A, B, and C, and 3 DNA chains: D, E, and F. The chains A, B, D, and E describe two variants of the complex, one including nucleotide residues DA1 and DT8 of the chain D and DT1 and DA8 of the chain E; another including residues DT1 and DA8 of the chain D and DA1 and DT8 of the chain E. In the original entry, the residues , e.g, DA1 and DT1 of the ... The model 1 contains all atoms of the chain F except of having the altercode "B". ...
... All contacts alignment . ... Hydrophobic contacts . ... The ETS domain is approximately 85-90 aa DNA-binding domain, that specifically interacts with sequences containing the common core trinucleotide GGA. ... Many of the ETS proteins have been shown to be transcription activators, ETS proteins have been implicated in regulation of gene expression during a variety of biological processes, including growth control, transformation, T-cell activation, and developmental programs in many organisms. ...
... The Lambda C1 repressor consists of two domains connected by a linker: an N-terminal DNA-binding domain that also mediates interactions with RNA polymerase, and a C-terminal dimerisation domain [1]. ... Several different phage repressors from different helix-turn-helix families contain DNA-binding domains that adopt a similar topology. ... Bell C.E. , Frescura P. , Hochschild A. , Lewis M. Crystal structure of the lambda repressor C-terminal domain provides a model for cooperative operator binding. ...