PDBsum entry: 1ga5

Transcription/DNA

PDB id: 1ga5

Contents

Protein chains

82 a.a. *

78 a.a. *

DNA/RNA

Metals

_ZN ×8

Waters ×279

* Residue conservation analysis

PDB id:

1ga5

Name:

Transcription/DNA

Title:

Crystal structure of the orphan nuclear receptor rev- erb(alpha) DNA-binding domain bound to its cognate response element

Structure:

5'- d( Cp Ap Ap Cp Tp Ap Gp Gp Tp Cp Ap Cp Tp Ap Gp Gp Tp Cp Ap G)-3'. Chain: c, g. Engineered: yes. 5'- d( Cp Tp Gp Ap Cp Cp Tp Ap Gp Tp Gp Ap Cp Cp Tp Ap Gp Tp (5 It)p G)-3'. Chain: d, h.

Source:

Synthetic: yes. Other_details: synthesized optimal dr2 target. Other_details: synthesized optimal dr2 target complementary strand with 5-iodo-thymidine. Homo sapiens. Human. Organism_taxid: 9606. Gene: nr1d1 or thral or ear1 or hrev. Expressed in: escherichia coli bl21(de3).

Biol. unit:

Tetramer (from PQS)

Resolution:

2.40Å R-factor: 0.253 R-free: 0.299

Authors:

M.L.Sierk,Q.Zhao,F.Rastinejad

Key ref:

M.L.Sierk et al. (2001). DNA deformability as a recognition feature in the reverb response element. Biochemistry, 40, 12833-12843. PubMed id: 11669620 DOI: 10.1021/bi011086r

Date:

29-Nov-00 Release date: 16-Nov-01

Protein chains

P20393  (NR1D1_HUMAN) -  Nuclear receptor subfamily 1 group D member 1

Seq: 614 a.a.

Struc: 82 a.a.*

Protein chain

P20393  (NR1D1_HUMAN) -  Nuclear receptor subfamily 1 group D member 1

Seq: 614 a.a.

Struc: 78 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biological process: regulation of transcription, DNA-dependent (1 term)
• Biochemical function: DNA binding (6 terms)

DOI no: 10.1021/bi011086r

Biochemistry 40:12833-12843 (2001)

PubMed id: 11669620

DNA deformability as a recognition feature in the reverb response element.

M.L.Sierk, Q.Zhao, F.Rastinejad.

ABSTRACT

Most nuclear receptors recognize the same consensus hexameric sequence, AGGTCA. An important question has been how the various members of this transcription factor family distinguish identity features in these closely related DNA sites. We determined structures from several crystal forms of the RevErb-DNA complex and analyzed the patterns of protein-DNA interactions and DNA distortions. We found a significant and consistent DNA distortion at a TA step directly preceding the first consensus 5'-AGGTCA-3' recognition sequence. Importantly, while this base-pair sequence is associated with RevErb's high-affinity sites, there are no sequence-specific contacts formed with the protein. Our study shows that RevErb relies instead on the intrinsic geometry and flexibility of this TA site to make the required fit between the proteins' independent major groove and minor groove binding interactions, which occur on both sides of the TA step. Our findings extend the description of response element discrimination to include a role for sequence-dependent DNA deformations and suggest how other monomeric members of this superfamily, such as NGFI-B, SF-1, and ROR, could also recognize unique geometric features in their DNA targets.