PDBsum entry: 1per

Transcription/DNA

PDB id: 1per

Contents

Protein chains

63 a.a. *

DNA/RNA

Waters ×40

* Residue conservation analysis

PDB id:

1per

Name:

Transcription/DNA

Title:

The complex between phage 434 repression DNA-binding domain and operator site or3: structural differences between consensus and non-consensus half-sites

Structure:

DNA (5'- d( Ap Ap Gp Tp Ap Cp Ap Gp Tp Tp Tp Tp Tp Cp Tp Tp G p Tp Ap T)-3'). Chain: a. Engineered: yes. DNA (5'- d( Tp Ap Tp Ap Cp Ap Ap Gp Ap Ap Ap Ap Ap Cp Tp Gp T p Ap Cp T)-3'). Chain: b.

Source:

Synthetic: yes. Phage 434. Organism_taxid: 10712

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.187

Authors:

D.W.Rodgers,S.C.Harrison

Key ref:

D.W.Rodgers and S.C.Harrison (1993). The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites. Structure, 1, 227-240. PubMed id: 8081737 DOI: 10.1016/0969-2126(93)90012-6

Date:

09-Nov-93 Release date: 31-Jan-94

Protein chains

P16117  (RPC1_BP434) -  Repressor protein CI (Fragment)

Seq: 95 a.a.

Struc: 63 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: DNA binding (2 terms)

DOI no: 10.1016/0969-2126(93)90012-6

Structure 1:227-240 (1993)

PubMed id: 8081737

The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites.

D.W.Rodgers, S.C.Harrison.

ABSTRACT

BACKGROUND: The repressor of phage 434 binds to a set of operator sites as a homodimer. Its relative affinities for these sites determine the switch from lysogenic to lytic growth. The six 434 operator sites (OR1, OR2, OR3, OL1, OL2 and OL3) have a particularly simple organization; all are 14 base pairs long, with a conserved 5'-ACAA sequence symmetrically placed at either end, and a variable central six base pairs. OR3 is unique among naturally-occurring 434 operator sites in that it contains a non-consensus base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA sequence. Comparisons among structures of the 434 repressor DNA-binding domain, R1-69, bound to various operator sites, allow us to analyze differential specificity in regulatory complexes of this kind. RESULTS: We have determined the structure at 2.5 A resolution of a complex of R1-69 with DNA containing the OR3 site and compared it with previously studied complexes of R1-69 bound to OR1 and OR2. There are surprisingly extensive structural differences between the consensus and non-consensus half-sites of OR3 with respect to their interactions with R1-69, including a shift in the DNA backbone and a small rotation of the entire R1-69 monomer. CONCLUSIONS: Recognition of the base pair difference that is critical for the 434 regulatory switch involves a number of amino acid residues, not just the one or two side chains in direct contact with the G-C base pair. Moreover, the repressor imposes a somewhat altered DNA conformation on the non-consensus half-site.