PDBsum entry 1g2f

Transcription/DNA

PDB id: 1g2f

Contents

Protein chains

89 a.a. *

DNA/RNA

Metals

_ZN ×6

Waters ×227

* Residue conservation analysis

PDB id:

1g2f

Name:

Transcription/DNA

Title:

Structure of a cys2his2 zinc finger/tata box complex (tatazf;clone #6)

Structure:

5'-d( Gp Ap Cp Gp Cp Tp Ap Tp Ap Ap Ap Ap Gp Gp Ap G)-3'. Chain: a, d. Engineered: yes. 5'-d( Tp Cp Cp Tp Tp Tp Tp Ap Tp Ap Gp Cp Gp Tp Cp C)-3'. Chain: b, e. Engineered: yes. Tata box zinc finger protein. Chain: c, f. Engineered: yes

Source:

Synthetic: yes. Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: protein selected by phage display

Biol. unit:

Trimer (from PQS)

Resolution:

2.00Å R-factor: 0.233 R-free: 0.263

Authors:

S.A.Wolfe,R.A.Grant,M.Elrod-Erickson,C.O.Pabo

Key ref:

S.A.Wolfe et al. (2001). Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Structure, 9, 717-723. PubMed id: 11587646 DOI: 10.1016/S0969-2126(01)00632-3

Date:

18-Oct-00 Release date: 07-Sep-01

Protein chains

P08046  (EGR1_MOUSE) -  Early growth response protein 1 from Mus musculus

Seq: 533 a.a.

Struc: 89 a.a.*

* PDB and UniProt seqs differ at 18 residue positions (black crosses)

DNA/RNA chains

G-A-C-G-C-T-A-T-A-A-A-A-G-G-A-G 16 bases

T-C-C-T-T-T-T-A-T-A-G-C-G-T-C-C 16 bases

G-A-C-G-C-T-A-T-A-A-A-A-G-G-A-G 16 bases

T-C-C-T-T-T-T-A-T-A-G-C-G-T-C-C 16 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/S0969-2126(01)00632-3

Structure 9:717-723 (2001)

PubMed id: 11587646

Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes.

S.A.Wolfe, R.A.Grant, M.Elrod-Erickson, C.O.Pabo.

ABSTRACT

BACKGROUND: Several methods have been developed for creating Cys2His2 zinc finger proteins that recognize novel DNA sequences, and these proteins may have important applications in biological research and gene therapy. In spite of this progress with design/selection methodology, fundamental questions remain about the principles that govern DNA recognition. One hypothesis suggests that recognition can be described by a simple set of rules--essentially a "recognition code"--but careful assessment of this proposal has been difficult because there have been few structural studies of selected zinc finger proteins. RESULTS: We report the high-resolution cocrystal structures of two zinc finger proteins that had been selected (as variants of Zif268) to recognize a eukaryotic TATA box sequence. The overall docking arrangement of the fingers within the major groove of the DNA is similar to that observed in the Zif268 complex. Nevertheless, comparison of Zif268 and the selected variants reveal significant differences in the pattern of side chain-base interactions. The new structures also reveal side chain-side chain interactions (both within and between fingers) that are important in stabilizing the protein-DNA interface and appear to play substantial roles in recognition. CONCLUSIONS: These new structures highlight the surprising complexity of zinc finger-DNA interactions. The diversity of interactions observed at the protein-DNA interface, which is especially striking for proteins that were all derived from Zif268, challenges fundamental concepts about zinc finger-DNA recognition and underscores the difficulty in developing any meaningful recognition code.

Selected figure(s)

Figure 4.
Figure 4. Side Chain-Side Chain Interactions within the Recognition Helix Stabilize the Protein-DNA InterfaceIn the selected TATA proteins, whenever glutamine was present at position 6 of finger 2, threonine was absolutely conserved at position 2 [7]. The structure of TATA[ZF]* explains this preference; the g-methyl group of Thr-48 and the methyl group of T8 pack against opposite faces of Gln-52. Presumably, this stabilizes the interaction of Gln-52 with A7. This is analogous to the interfinger interaction described between fingers 1 and 2 of TATA[ZF] in Figure 3a. (Coloring scheme is the same as in Figure 2.)

The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 717-723) copyright 2001.

Figure was selected by an automated process.