PDBsum entry 2kae

Transcription/DNA

PDB id: 2kae

Contents

Protein chain

56 a.a. *

DNA/RNA

Metals

_ZN

* Residue conservation analysis

PDB id:

2kae

Name:

Transcription/DNA

Title:

Data-driven model of med1:dna complex

Structure:

Gata-type transcription factor. Chain: a. Fragment: unp residues 111-166. Engineered: yes. 5'-d( Dcp Dgp Dgp Dap Dap Dap Dap Dgp Dtp Dap Dtp Dap Dcp D tp Dtp Dtp Dtp Dcp Dcp Dg)-3'. Chain: c, b. Engineered: yes

Source:

Caenorhabditis elegans. Nematode. Organism_taxid: 6239. Gene: med-1, t24d3.1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

NMR struc:

10 models

Authors:

J.A.Lowry,R.Gamsjaeger,S.Thong,W.Hung,A.H.Kwan,G.Broitman-Maduro, J.M.Matthews,M.Maduro,J.P.Mackay

Key ref:

J.A.Lowry et al. (2009). Structural Analysis of MED-1 Reveals Unexpected Diversity in the Mechanism of DNA Recognition by GATA-type Zinc Finger Domains. J Biol Chem, 284, 5827-5835. PubMed id: 19095651 DOI: 10.1074/jbc.M808712200

Date:

04-Nov-08 Release date: 06-Jan-09

Protein chain

Q9GSP3  (Q9GSP3_CAEEL) -

DNA/RNA chains

C-G-G-A-A-A-A-G-T-A-T-A-C-T-T-T-T-C-C-G 20 bases

C-G-G-A-A-A-A-G-T-A-T-A-C-T-T-T-T-C-C-G 20 bases

DOI no: 10.1074/jbc.M808712200

J Biol Chem 284:5827-5835 (2009)

PubMed id: 19095651

Structural Analysis of MED-1 Reveals Unexpected Diversity in the Mechanism of DNA Recognition by GATA-type Zinc Finger Domains.

J.A.Lowry, R.Gamsjaeger, S.Y.Thong, W.Hung, A.H.Kwan, G.Broitman-Maduro, J.M.Matthews, M.Maduro, J.P.Mackay.

ABSTRACT

MED-1 is a member of a group of divergent GATA-type zinc finger proteins recently identified in several species of Caenorhabditis. The med genes are transcriptional regulators that are involved in the specification of the mesoderm and endoderm precursor cells in nematodes. Unlike other GATA-type zinc fingers that recognize the consensus sequence (A/C/T)GATA(A/G), the MED-1 zinc finger (MED1zf) binds the larger and atypical site GTATACT(T/C)(3). We have examined the basis for this unusual DNA specificity using a range of biochemical and biophysical approaches. Most strikingly, we show that although the core of the MED1zf structure is similar to that of GATA-1, the basic tail C-terminal to the zinc finger unexpectedly adopts an alpha-helical structure upon binding DNA. This additional helix appears to contact the major groove of the DNA, making contacts that explain the extended DNA consensus sequence observed for MED1zf. Our data expand the versatility of DNA recognition by GATA-type zinc fingers and perhaps shed new light on the DNA-binding properties of mammalian GATA factors.

Selected figure(s)

Figure 1.
Sequences used in this study. A, amino acid sequences of the GATA-type zinc fingers from C. elegans MED-1, chicken (c) GATA-1, murine (m) GATA-1, human (h) GATA-1/2/3, and A. nidulans AreA. Light and dark gray areas indicate conserved and identical residues, respectively. The zinc ligands are indicated with asterisks, and the secondary structure of the chicken GATA-1 zinc finger is indicated. Numbering is for full-length proteins. B, sequence of the 20-bp oligonucleotide used in this work. The MED-1-binding site is underlined.

Figure 5.
Data-driven model of the MED1zf·DNA. A, overlay of the 10 lowest energy HADDOCK structures of the MED1zf·DNA. B, ribbon diagram of the lowest energy structure from HADDOCK and detailed view of helix 2 and the N-terminal part (β2-β3 region) of MED1zf. Residues colored in red, green, and blue of the β2-β3 region, helix 1, and the newly formed helix 2 of MED1zf, respectively, make specific interactions with the DNA. The zinc atom and coordinating cysteines are shown in gray. C, schematic summary of the specific protein-DNA contacts. Bases that are specifically recognized by MED1zf are colored orange; interactions are indicated by arrows in the same colors as in A and B. D, comparison of the DNA-binding modes of MED1zf and GATA-1 (Protein Data Bank code 1GAT) (14). Residues that specifically contact DNA are colored as in A and B.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 5827-5835) copyright 2009.

Figures were selected by an automated process.