PDBsum entry 1ea4

Gene regulation/DNA

PDB id: 1ea4

Contents

Protein chains

42 a.a.

41 a.a.

43 a.a.

44 a.a.

45 a.a.

DNA/RNA

Waters ×101

PDB id:

1ea4

Name:

Gene regulation/DNA

Title:

Transcriptional repressor copg/22bp dsdna complex

Structure:

Transcriptional repressor copg. Chain: a, b, d, e, f, g, h, j, k, l. Fragment: DNA-binding protein. Synonym: repa protein. Engineered: yes. DNA (5'-d( Tp Ap Ap Cp Cp Gp Tp Gp Cp Ap Cp Tp Cp Ap Ap Tp Gp Cp Ap Ap Tp C)-3'). Chain: u, w, y. Fragment: 22bp ssdna - first strand.

Source:

Streptococcus agalactiae. Organism_taxid: 1311. Cellular_location: plasmid pmv158. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

Biol. unit:

Dimer (from PDB file)

Resolution:

2.95Å R-factor: 0.230 R-free: 0.307

Authors:

F.X.Gomis-Rueth,M.Costa,M.Sola,P.Acebo,R.Eritja,M.Espinosa,G.D.Solar, M.Coll

Key ref:

M.Costa et al. (2001). Plasmid transcriptional repressor CopG oligomerises to render helical superstructures unbound and in complexes with oligonucleotides. J Mol Biol, 310, 403-417. PubMed id: 11428897 DOI: 10.1006/jmbi.2001.4760

Date:

05-Nov-00 Release date: 05-Jul-01

Protein chain

P13920  (COPG_STRAG) -  Protein CopG from Streptococcus agalactiae

Seq: 45 a.a.

Struc: 42 a.a.

Protein chain

P13920  (COPG_STRAG) -  Protein CopG from Streptococcus agalactiae

Seq: 45 a.a.

Struc: 41 a.a.

Protein chain

P13920  (COPG_STRAG) -  Protein CopG from Streptococcus agalactiae

Seq: 45 a.a.

Struc: 43 a.a.

Protein chains

P13920  (COPG_STRAG) -  Protein CopG from Streptococcus agalactiae

Seq: 45 a.a.

Struc: 44 a.a.

Protein chains

P13920  (COPG_STRAG) -  Protein CopG from Streptococcus agalactiae

Seq: 45 a.a.

Struc: 45 a.a.

DNA/RNA chains

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

A-G-A-T-T-G-C-A-T-T-G-A-G-T-G-C-A-C-G-G-T 21 bases

T-A-A-C-C-G-T-G-C-A-C-T-C-A-A-T-G-C-A-A-T-C 22 bases

A-G-A-T-T-G-C-A-T-T-G-A-G-T-G-C-A-C-G-G-T-T 22 bases

A-A-C-C-G-T-G-C-A-C-T-C-A-A-T-G-C-A-A-T-C 21 bases

A-G-A-T-T-G-C-A-T-T-G-A-G-T-G-C-A-C-G-G-T 21 bases

DOI no: 10.1006/jmbi.2001.4760

J Mol Biol 310:403-417 (2001)

PubMed id: 11428897

Plasmid transcriptional repressor CopG oligomerises to render helical superstructures unbound and in complexes with oligonucleotides.

M.Costa, M.Solà, G.del Solar, R.Eritja, A.M.Hernández-Arriaga, M.Espinosa, F.X.Gomis-Rüth, M.Coll.

ABSTRACT

CopG is a 45 amino acid residue transcriptional repressor involved in the copy number control of the streptococcal plasmid pMV158. To do so, it binds to a DNA operator that contains a 13 bp pseudosymmetric DNA element. Binding of CopG to its operator results in repression, at the transcriptional level, of its own synthesis and that of the initiator of replication protein, RepB. Biochemical experiments have shown that CopG co-operatively associates to its target DNA at low protein:DNA ratios, completely protecting four helical turns on the same face of the double helix in both directions from the inverted repeat that constitutes the CopG primary target. This has been correlated with a CopG-mediated DNA bend of about 100 degrees. Here, we show that binding of CopG to DNA fragments containing the inverted repeat just at one end led to nucleation of the protein initiating from the inverted repeat. Nucleation extended to the entire fragment, with CopG-DNA contacts occurring on the same face of the DNA helix. The protein, the prototype for a family of homologous plasmid repressors, displays a homodimeric ribbon-helix-helix arrangement. It polymerises within the unbound crystal to render a continuous right-handed protein superhelix of homodimers, around which a bound double-stranded (ds) DNA could wrap. We have solved the crystal structure of CopG in complex with a 22 bp dsDNA oligonucleotide encompassing the cognate pseudosymmetric element. In the crystal, one protein tetramer binds at one face of the DNA with two parallel beta-ribbons inserted into the major groove. The DNA is bent about 50 degrees under compression of both major and minor grooves. A continuous right-handed complex helix made up mainly by protein-protein and some protein-DNA interactions is observed. The protein-protein interactions involve regions similar to those observed in the oligomerisation of the native crystals and those employed to set up the functional tetramer. A previously solved complex structure of the protein with a 19 bp dsDNA had unveiled a left-handed helical superstructure just made up by DNA interactions.

Selected figure(s)

Figure 2.
Figure 2. (a) Sequence of the double-stranded deoxyribooligonucleotide encompassing the 13 bp cognate IR sequence employed for co-crystallisation in the present work. The black box signifies the centre of the operator. (b) Stereo ribbon plot of the CopG dimer of dimers (in brown/blue and magenta/blue) in complex with the 22 bp dsDNA superimposed with its semitransparent Connolly surface. (c) Schematic organisation of the asymmetric unit contents (bright colours) transformed into their symmetry-equivalents via a crystallographic dyad (light colours).

Figure 5.
Figure 5. Superhelical oligomerisation of CopG in its complexes with (a) 19 bp dsDNA and (b) 22 bp dsDNA. Lateral stereo ribbon plots for each superhelix are displayed, so as the helical pitches and diameters. In (a) the continuous left-handed helix is based on dsDNA (superimposed with its semitransparent Connolly surface) interactions with no protein-protein contacts, whereas mainly protein-protein contacts result in a right-handed superhelix in (b), shown with the semitransparent Connolly surface of the protein part.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 310, 403-417) copyright 2001.

Figures were selected by an automated process.