PDBsum entry: 1lei

Transcription/DNA

PDB id: 1lei

Contents

Protein chains

273 a.a. *

312 a.a. *

DNA/RNA

Waters ×23

* Residue conservation analysis

PDB id:

1lei

Name:

Transcription/DNA

Title:

The kb DNA sequence from the hlv-ltr functions as an allosteric regulator of HIV transcription

Structure:

5'- d( Cp Tp Cp Ap Gp Gp Gp Ap Ap Ap Gp Tp Ap Cp Ap Gp A)-3'. Chain: c. Engineered: yes. Other_details: kb DNA. 5'- d( Tp Cp Tp Gp 5Itp Ap Cp 5Itp 5Itp 5Itp Cp Cp Cp Tp Gp Ap G)-3'. Chain: d.

Source:

Synthetic: yes. Mus musculus. House mouse. Organism_taxid: 10090. Gene: rela. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: nfkb1.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.70Å R-factor: 0.250 R-free: 0.284

Authors:

F.Chen-Park,D.B.Huang,G.Ghosh

Key ref:

F.E.Chen-Park et al. (2002). The kappa B DNA sequence from the HIV long terminal repeat functions as an allosteric regulator of HIV transcription. J Biol Chem, 277, 24701-24708. PubMed id: 11970949 DOI: 10.1074/jbc.M200007200

Date:

09-Apr-02 Release date: 15-Apr-03

Protein chain

Q04207  (TF65_MOUSE) -  Transcription factor p65

Seq: 549 a.a.

Struc: 273 a.a.*

Protein chain

P25799  (NFKB1_MOUSE) -  Nuclear factor NF-kappa-B p105 subunit

Seq: 971 a.a.

Struc: 312 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biological process: regulation of transcription (2 terms)
• Biochemical function: transcription factor activity (1 term)

DOI no: 10.1074/jbc.M200007200

J Biol Chem 277:24701-24708 (2002)

PubMed id: 11970949

The kappa B DNA sequence from the HIV long terminal repeat functions as an allosteric regulator of HIV transcription.

F.E.Chen-Park, D.B.Huang, B.Noro, D.Thanos, G.Ghosh.

ABSTRACT

NF-kappaB is an inducible transcription factor involved in the immune response, inflammation, and viral transcription. To address how the two NF-kappaB and three Sp1 binding sites of the human immunodeficiency virus (HIV) long terminal repeat (LTR) control multiple activator assembly and transcription, we first observed and compared unique conformations between the crystallographic structure of the NF-kappaB p50.p65 heterodimer bound to the uPA-kappaB target site to that of the p50.p65.HIV-kappaB complex. Next, cooperativity between two NF-kappaB molecules bound to tandem HIV-kappaB sequences was measured as well as that of NF-kappaB and transcription factor Sp1 when bound to adjacent sites. The cooperativity of hybrid HIV-LTR enhancers was measured with the 3' kappaB site converted to uPA-kappaB or to interferon beta gene enhancer kappaB. The hybrids were defective in transcriptional activator assembly and less active transcriptionally. These functional differences correlate with observed conformational differences and demonstrate that distinct kappaB DNA sequences function as allosteric regulators in a gene-specific manner.

Selected figure(s)

Figure 1.
Fig. 1. Comparison of B DNA sites. Shown are B sites from the immunoglobulin light chain enhancer gene/HIV promoter (HIV), the urokinase plasminogen activator gene ( uPA), and the PRDII region of the interferon enhancer (IFN ). The uPA- B site differs from the consensus at the +1 and +3 positions and from the HIV- B at the 1, 0, +1, and +3 positions.

Figure 6.
Fig. 6. Stereo figure of two NF- B molecules modeled on HIV-LTR DNA. Two NF- B molecules are modeled on a 26-mer B-DNA (yellow) with the two B sites of the HIV LTR by a simple least squares superposition of the B DNA's phosphate backbone. The C traces are of two NF- B proteins in their HIV- B DNA-bound conformations (gray and blue). Also included is an overlay of a NF- B molecule in its uPA- B bound conformation (purple) bound to the 3' B site. White circles indicate areas of potential interactions between the two proteins.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 24701-24708) copyright 2002.

Figures were selected by the author.