Biochemistry 3107 - Fall 2001

DNA-binding Proteins

A Note on DNA-binding Proteins

In our course, we will encounter examples of different types of DNA-binding protein. The most common andbest studies DNA-binding proteins are the Zinc finger proteins, the Helix-turn-helix proteins, and the Leucine zipper proteins.

[MVH28-23]

TBP-binding domain

This domain is found in the TATA-box binding protein which is a subunit of the eukaryotic transcription factor, TFIID. This protein is somewhat unusual in that it binds to the minor groove of DNA.

[25-13a] [25-13a]

	Click on the image to see a large view of TBP associated with DNA. Two complexes are shown. On the left, you can see how the protein interacts in the minor groove.
Image from:

 

Zinc finger domain

This domain is common in eukaryotic DNA-binding proteins. It was first noticed in the eukaryotic transcription factor, TFIIIA.

[23-35] [MVH28-22]

TFIIIA contains 9 repeated modules, each of which contains two Cysteine and two Histidine residues. These four residues chelate one Zn++ ion. Each finger is bound in the major groove of B-DNA.

[6-35] [S37-32]

View a Chime Tutorial on Zn finger DNA binding proteins from Massey University, New Zealand.

 

Helix-turn-helix domain

This motif was first noticed as a feature of the crystal structure of the bacteriophage l Cro protein. The structure of this small regulatory protein contained two a-helices separated by 34 Å - the pitch of a DNA double helix. Model building studies showed that these two a-helices would fit into two successive major grooves.

[23-32a]

As the structures of a number of other bacterial regulatory proteins (the CRP protein and the bacteriophage l cI repressor) were solved, the same structural motif - called a helix-turn-helix - was observed.

It consists of two a-helices separated by a short turn (it is not a b turn). One helix binds to recognition elements within the major groove of DNA; the other helps to keep the binding helix properly positioned with respect to the rest of the molecule.

[23-32b]

This motif, common in bacterial DNA-binding proteins, also occurs in the eukaryotic homeobox proteins.

View a Chime Tutorial on the CRP (aka CAP) DNA binding protein from Massey University, New Zealand.

 

Leucine Zipper domains

This domain is an important feature of many eukaryotic regulatory proteins.

Leucine is an hydrophobic amino acid. When it occurs at every seventh position of an a-helix, the aliphatic side-chains are all oriented on the same side of the helix and they can interact with another such helix to form a coiled coil type of structure.

[23-38a][23-38b]

The GCN4 transcription activator in yeast is a dimer in which the leucine zipper region helps to position the two basic regions that bind to the DNA recognition sequence.

Structure of the GCN4 basic domain-leucine zipper bound to ATF/CREB target site DNA from TJ Richmond Lab at ETH Zurich A Chime animation on The GCN4 Basic Region Leucine Zipper a BIOCHEM 153BH honors project by Thao Tran at UCLA.

A variation on this structural theme is provided by the Helix-Loop-Helix binding motif. In this case, the basic DNA-binding helices are connected to the dimerization helices by a short loop.

[Max -a] [Max -b]

The AP1 activator is a heterodimer of two proteins: Jun and Fos.

The ATF-CREB family consists of 13 different monomers that can form a total of 78 different heterodimers.

View a Chime Tutorial on AP1 from The University of Birmingham School of Medicine, England.

 

CLASSIFICATION

The most recent update of the transcription factor database lists 2785 entries. Many of these are homologous proteins from different species, nevertheless this number is indicative of the vast number of transcription factors now known that regulate the expression of eukaryotic genes.

The following table lists the categories of transcription factor and gives some important examples.

1 Superclass: Basic Domains
1.1 Class: Leucine zipper factors (bZIP)	1.1.1 Family: AP-1(-like) components includes Jun, Fos, AP-1(-like) (e.g. GCN4), CRE-BP/ATF  1.1.2 Family: CREB includes CREB, ATF-1, 1.1.3 Family: C/EBP-like factors and 4 other families
1.2 Class: Helix-loop-helix factors (bHLH)	1.2.2 Family: Myogenic transcription factors and 8 other families
1.3 Class: Helix-loop-helix / leucine zipper factors (bHLH-ZIP)	1.3.2 Family: Cell-cycle controlling factors includes Myc, Max, and 1 other family
1.4 Class: NF-1
1.5 Class: RF-X
1.6 Class: bHSH
2 Superclass: Zinc-coordinating DNA-binding domains
2.1 Class: Cys4 zinc finger of nuclear receptor type	2.1.1 Family: Steroid hormone receptors 2.1.2 Family: Thyroid hormone receptor-like factors includes RAR, RXR, Vitamin D receptor, PPAR, Knirps
2.2 Class: diverse Cys4 zinc fingers	4 families
2.3 Class: Cys2His2 zinc finger domain	2.3.1 Family: Ubiquitous factors includes TFIIIA, Sp1 2.3.2 Family: Developmental / cell cycle regulators includes Krüppel, Hunchback and 3 other families
2.4 Class: Cys6 cysteine-zinc cluster	2.4.1 Family: Metabolic regulators in fungi
2.5 Class: Zinc fingers of alternating composition	2 families
3 Superclass: Helix-turn-helix
3.1 Class: Homeo domain	3.1.1 Family: Homeo domain only includes Antp, Ubx, Engrailed, Eve, 3.1.2 Family: POU domain factors includes Oct-1, Oct-2 and 2 other families
3.2 Class: Paired box
3.3 Class: Fork head / winged helix	3.3.1 Family: Developmental regulators includes forkhead and 2 other families
3.4 Class: Heat shock factors
3.5 Class: Tryptophan clusters	3.5.1 Family: Myb and 2 other families
3.6 Class: TEA domain
4 Superclass: beta-Scaffold Factors with Minor Groove Contacts
4.1 Class: RHR (Rel homology region)	4.1.1 Family: Rel/ankyrin includes NF-kappaB1 and 2 other families
4.2 Class: STAT
4.3 Class: p53
4.4 Class: MADS box	4.4.1 Family: Regulators of differentiation includes Agamous, AP1, Deficiens, AP3 and 2 other families
4.5 Class: beta-Barrel alpha-helix transcription factors
4.6 Class: TATA-binding proteins	4.6.1 Family: TBP
4.7 Class: HMG
4.8 Class: Heteromeric CCAAT factors
4.9 Class: Grainyhead
4.10 Class: Cold-shock domain factors
4.11 Class: Runt
0 Superclass: Other Transcription Factors
0.1 Class: Copper fist proteins
0.2 Class: HMGI(Y)
0.3 Class: Pocket domain	0.3.1 Family: Rb includes Rb - retinoblastoma 1 other family
0.4 Class: E1A-like factors	E1A
0.5 Class: AP2/EREBP-related factors	0.5.1 Family: AP2 includes AP2 2 other families