dna binding domains
DESCRIPTION
DNA binding domain with Helix turn Helix structuresTRANSCRIPT
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DNA binding domain with Helix turn Helix structuresNaveed asif (MS)BiochemistryCOMSATS-IslamabadPakistan2013-14
It’s a DOMAIN that binds to DNA
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•The proteins that Bind to DNA consist of fallowing parts
1-Ligend binding Domain3-Activation or repression Domain (C-terminal)2-DNA binding Domain (N-terminal)
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•Presentation constitutes
1-Structure of Helix turns Helix Domain2-Its interaction with DNA3-Its Functionsa-In Activatorsb-In Repressors
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•1-Sturcture of Helix turn Helix Domain
Secondary structure (Helix) + Secondarystructure(Helix)
Supersecondary structure (motif) Mofit + Motif
Domain
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• Structure of helix turn helix motif
Two alpha helixes joined by a turnDIFFERENCE between turn & loop
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• Structure of a loop
Difference1-Loop is larger than turn. 2-loop has 7 to 16 amino acids. turn has 4 to 6 amino acidsSimilaritiesBoth has charged amino acids
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•General Mechanism of formation of a Domain
Secondary structure (Helix or Beta) + Secondary structure (HelixorBeta) Supersecondary structure (motif) Mofit + Motif
Domain
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•Formation of Complex Domains
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•BACK to helix turn helix motife.g. HOMEO-DOMAIN
They are formed by homeoboxes. Homeoboxes are conserved sequences of 180 base pairs; the proteins formed by these boxes give rise to domains that are called homeodomains
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• Mechanism of interaction with DNA
PARTS of HELIX turn HELIX motif
1-HORIZONTAL one is recognition helix
ANGEL 90◦2-VETICAL helix is going to interact with back bone3-Recognition helix goes into the major groove C-terminal (Recognition helix) and-N terminal (helix that interact with backbone)
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• Mechanism Cont.Interaction is between charged amino acids, phosphate back bone and nitrogenous basesArginine (positively charged), Asparagines-Asn (neutral) and serine-Ser (neutral)
THIS BINDING COULD BE OF ACTIVATOR HTH motif
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•Mechanism cont.HTH-Motif(Charge on Amino Acids)CHARGE on the AMINO ACID plays the key roleNeutral, (--) and (+)1-This untimely effect the polypeptide polarity2-this also gives a sequence specific binding between DNA & ProteinAnd can be modified1-Phosphorilation2-Aceylation3-methylation These modifications are very important in activator and repressor proteins
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•FunctionsTranscription Repression & Activation
1-Repression function of helix turn helix motif2-Activation function of helix turn helix motife.g.:- Lac repressor &CAP(catabolite activator
protein)
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• Normal• DNA
• ↓ bending
• ↓ Bending
• ↓ ●• ↓
•Lac repressor (helix turn helix motif)SEQUENCE
Glutamic acid (negative charge)Asparagines(neutral) Leucine(neutral)Under the normal circumstances repressor keeps on binding the operator.It BENDS the DNAWhat type of bending?No Transcription.
Lactose→ AllolactoseAllolactose binds to the allostaric site→ Conformational changeWhat kind of change? The distance between the two helix’s changesNow repressor is unable to bind leading to transcription
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• Normal DNA• ↓• Open bend• ↓• ●
SEQUENCE Arginine (Positively charged) Asparagines (neutral) Serine (neutral)
cAMP INTERACTIONMechanism
CAP+cAMPConfirmation change in the CAP Protein What change?Distance between the two helix’s changesNow DNA bendsActivates the Transcription
•2-CAP (Catabolite Activator Protein) helix turn helix Motif
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Thanks for your PATEINCE ReferencesMolecular genetics lectures, Dr. SaeedCOMSATS-Islamabad, PakistanBiosciences resource; Massey University, New ZealandIshaque P.K , Pondicherry University