Question

DNA‑binding domains recognize and bind to specific DNA sequences.

Complete the sentences. The homeodomain is also called the homeobox domain. Not all words will be used. Two terms will be used more than once.

A

1.)

contains a metal ion in coordination with two cysteine and two histidine residues or with four

cysteine residues.

DNA–protein binding generally occurs in the

2.)

of DNA.

The

3.) , found in eukaryotes, contains a small DNA‑binding region similar to the

helix‑turn‑helix motif.

The amino acids of the DNA‑binding domain generally form

4.)

with DNA.

The binding of a metal ion, as well as the presence of a hydrophobic core, stabilizes the

5.)

motif.

6.) is a common residue that interacts with the bases in DNA.

The

7.)

motif, common to many prokaryotic proteins, contains a recognition helix that protrudes

from the DNA‑binding domain and interacts with the

8.) of the DNA‑binding site.

answer bank

Minor groove Val Glu Hydrogen bond helix turn helix

Covalent Bond Zink finger Homeodomain Major groove

Answer 1

1. A zinc finger contains a metal ion in coordination with two cysteine and two histidine residues or with four cysteine residues.
2. DNA-protein binding generally occurs in the major groove of DNA. DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair.
3. The homeodomain, found in eukaryotes, contains a small DNA-binding region similar to the helix-turn-helix motif. homeodomain motifs are found in Homeobox transcription factors. They are sequence-specific DNA binding proteins that regulate transcription. They are characterized by a helix-turn-helix DNA-binding motif which is encoded by the 180 bp homeobox sequence element.
4. The amino acids of the DNA-binding domain generally form Hydrogen bond with the DNA. Most protein-DNA interactions are non-covalent in nature and are generally hydrogen bonding or hydrophobic interactions between the protein and the DNA base pairs.
5. The binding of a metal ion, as well as presence of a hydrophobic core stabilizes the zinc finger motif. The zinc finger consists of two anti-parallel beta sheets and a right handed alpha-helix. There are characteristic Cys2 His2 or Cys4 residues that are involved in coordination with the Zn2+ ion. The turn between two beta sheets has a hydrophobic core formed due to interactions between Phe and Leu amino acids present in that spatial conformation. This region is where Zn ion is bound.
6. Valine is a common residue that interacts with the bases in DNA. Interaction between amino acids and functional groups present in the DNA bases or negative charges of the phosphate backbone is the driving force that allows DNA binding proteins to bind to a DNA sequence. Nitrogenous bases are hydrophobic in nature and will interact with similar nature amino acid residues like valine and not glutamic acid (negatively charged).
7. The helix-turn-helix motif, common to many prokaryotic proteins, contain a recognition helix that protrudes from the DNA-binding domain and interacts with the major groove of the DNA-binding site. HLH motif was one ofthr first DNA binding domain to be discovered. It is present in proteins like cro repressor