mitchell - eukaryotic transcription

Question 1

name 3 DNA-BPs

Answer 1

Zn finger
Homeodomain fold
Basic leucine zipper

Question 2

describe the role of the homeodomain fold and its structure

Answer 2

dimer
each monomer contains recog helix
morphogenesis related 
involved in anterior-posterior development 
Hox genes encode homeodomain proteins

Question 3

describe the role of Zn fingers and its structure

Answer 3

versatile functions: interacts with DNA/RNA/protein 
beta-beta-alpha around Zn ion
recog helix binds to nt triplet at -1,2,3,6
Cys2His2
multiple Zn fingers
bind DNA as monomers
Cys4
2 Zn fingers
dimers
1 monomer recog specific nt's 
1 monomer forms Zn dimer

Question 4

describe the structure of the basic leucine zipper

Answer 4

coiled coil dimers
linked amphipathic helices - Leu locks together top bit with h.phobic interactions
leucine controls the dimerisation process
basic (+) residues at bottom allow dna binding - grip dna at adjacent major grooves

Question 5

name 4 RNA-binding domains

Answer 5

RNA recognition motif
KH domains
dsRNA binding domain
Zn finger

Question 6

describe binding and structure of the RNA recog motif

Answer 6

euks
4 beta and 2 alpha
RNA binding to 3-4 residues mediated by h.phobic stacking in beta and h-bonding between basic res and sug-P backbone
high affinity
either in multiple copies or interacts with other RNA binding domains

Question 7

describe binding and structure of the KH domain

Answer 7

all kingdoms
ssRNA/ssDNA
3 alpha and 3 beta - forms cleft with GXXG loop
4 bases recog by residues in cleft by electrostatic interactions and shape complementarity

Question 8

describe binding and structure of the dsRNA binding domain

Answer 8

found in range of proteins
interact with dsRNA in base-independent way - sugP backbone interactions and 2’ OH ribose interactions
shape recognition between 2 minor grooves and 1 major

Question 9

describe binding and structure of the Zn finger in RNA binding domains

Answer 9

C2H2 - multiple Zn fingers
identical residues in TFIIIA bind major DNA/loops 5S rRNA
Zn fingers of TISIId and mRNA - h bonding bases and polypeptide backbone