The document discusses the helix-turn-helix (HTH) and helix-loop-helix (HLH) motifs, which are critical for DNA binding in various proteins. HTH is characterized by two alpha helices that bind to the DNA's major groove and is mainly found in bacterial regulatory proteins, while HLH consists of two helices separated by a flexible loop, often found in eukaryotic transcription factors. Both motifs play significant roles in gene regulation and development, including implications in cancer through certain transcription factors.

1. HELIX- TURN- HELIX
&
HELIX- LOOP- HELIX
BIOTECHNOLOGY
- BY- NAREN
YADAV

2. DNA – Binding Domain
A DNA-binding domain (DBD) is an
independently folded protein domain that
contains at least one motif that recognizes
double- or single-stranded DNA. A DBD can
recognize a specific DNA sequence
(a recognition sequence) or have a general
affinity to DNA.
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3. Types of DNA-Binding Motifs
• 1. Steroid Receptor
• 2. Zinc Fingers
• 3. Leucine Zipper
• 4. Homeodomain
• 5.HELIX-TURN-HELIX
• 6.HELIX-LOOP-HELIX
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4. Helix-turn-helix
• In proteins, the helix-turn-helix (HTH) is a
major structural motif capable of
binding DNA.
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5. DISCOVERY
• The discovery of the helix-turn-helix
motif was based on similarities
between several genes
encoding transcription regulatory
proteins from bacteriophage
lambda and Escherichia coli: Cro, CAP,
and λ repressor, which were found to
share a common 20-25 amino
acid sequence that facilitates DNA
recognition. 5

6. EXAMPLE
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The λ repressor of
bacteriophage
lambda employs a
helix-turn-helix (left;
green) to
bindDNA (right; blue
and red).

7. STRUCTURE
• The structure consist of two α helices joined
by a short strand of amino acid.
• The recognition and binding to DNA by
helix-turn-helix proteins is done by the
two α helices, one occupying the N-
terminal end of the motif, the other at
the C-terminus.
• In most cases, such as in the Cro
repressor, the second helix contributes
most to DNA recognition, and hence it is
often called the "recognition helix".
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8. Helix-turn-helix
C-terminal binds to major groove, N-terminal
helps to position the complex
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9. FUNCTION
 The helix-turn-helix (HTH) is a major structural
motif capable of binding DNA. It is found in
many proteins that regulate gene expression.
 It binds to the major groove of DNA through
a series of hydrogen bonds and various Van
der Waals interactions with exposed bases.
The other α helix stabilizes the interaction
between protein and DNA, but does not play
a particularly strong role in its recognition.
 The recognition helix and its preceding helix
always have the same relative orientation.
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11. CLASSIFICATION OF HELIX
TURN HELIX
Di-helical
Tri-helical
Tetra-helical
Winged helix-turn-helix
Other modified helix-turn-helix motifs
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12. Helix-turn-helix
review
LOCATION
•Bacterial
regulatory
proteins,
•Related motifs
in eukaryotic
proteins.
CHARACTERIST
-ICS
•Two alpha
helices
BINDING SITE
IN DNA
•Major groove
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13. Helix-loop-helix
- The helix-loop-helix binding motif
consists of two alpha helices separated
by a loop of amino acids.
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14. STRUCTURE
-Two polypeptide chains with the motif
join to form a functional DNA-binding
protein.
- A highly basic set of amino acids in one
of the helices binds to the DNA.
- Transcription factor including this
domain are in dimeric form.
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15. CONTINUE…
• In general, one helix is smaller, and,
due to the flexibility of the loop, allows
dimerization by folding and packing
against another helix.
• The larger helix typically contains the
DNA-binding regions.
• bHLH proteins typically bind to
a consensus sequence called an E-box,
CANNTG.
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16. FUNCTION
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 bHLH transcription factors are often
important in development or cell
activity. BMAL1-Clock is a core
transcription complex in the
molecular circadian clock.
 Other genes, like c-Myc and HIF-1,
have been linked to cancer due to
their effects on cell growth and
metabolism.

17. REGULATION
• Since many bHLH transcription
factors are heterodimeric, their activity
is often highly regulated by the
dimerization of the subunits.
• One subunit's expression or availability
is often controlled, whereas the other
subunit is constitutively expressed.
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18. 18

19. Helix-loop-helix
review
LOCATION
•Eukaryotic
protein
CHARACTERIST
-ICS
•Two alpha
helices
separated by a
loop of amino
acids.
BINDING SITE IN
DNA
•Major groove
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20. EXAMPLES
• AhR,BMAL-1-CLOCK,C-Myc,
• N-Myc,MyoD,Myf5,Scleraxis,
• Neurogenis, etc…
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21. •THANK YOU
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