PDBsum entry 2ipr

DNA binding protein

PDB id: 2ipr

Contents

Protein chains

127 a.a. *

Waters ×251

* Residue conservation analysis

PDB id:

2ipr

Name:

DNA binding protein

Title:

Origin binding domain of the sv40 large t antigen (residues 131-259). P21 crystal form

Structure:

Large t antigen. Chain: a, b. Fragment: origin binding domain (residues 131-259). Engineered: yes

Source:

Simian virus 40. Organism_taxid: 10633. Strain: 776. Gene: large t antigen. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Monomer (from PQS)

Resolution:

1.50Å R-factor: 0.179 R-free: 0.204

Authors:

D.Martynowski,E.Bochkareva,A.Bochkarev

Key ref:

E.Bochkareva et al. (2006). Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA. EMBO J, 25, 5961-5969. PubMed id: 17139255 DOI: 10.1038/sj.emboj.7601452

Date:

12-Oct-06 Release date: 12-Dec-06

Protein chains

Q98ZP7  (Q98ZP7_SV40) -  Large T antigen from Simian virus 40

Seq: 537 a.a.

Struc: 127 a.a.

Enzyme reactions

• Enzyme class: E.C.5.6.2.4 - Dna 3'-5' helicase.

DOI no: 10.1038/sj.emboj.7601452

EMBO J 25:5961-5969 (2006)

PubMed id: 17139255

Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA.

E.Bochkareva, D.Martynowski, A.Seitova, A.Bochkarev.

ABSTRACT

The large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori) in simian virus 40 (SV40). Here, we determined the crystal structures of the T-ag origin-binding domain (OBD) in apo form, and bound to either a 17 bp palindrome (sites 1 and 3) or a 23 bp ori DNA palindrome comprising all four GAGGC binding sites for OBD. The T-ag OBDs were shown to interact with the DNA through a loop comprising Ser147-Thr155 (A1 loop), a combination of a DNA-binding helix and loop (His203-Asn210), and Asn227. The A1 loop traveled back-and-forth along the major groove and accounted for most of the sequence-determining contacts with the DNA. Unexpectedly, in both T-ag-DNA structures, the T-ag OBDs bound DNA independently and did not make direct protein-protein contacts. The T-ag OBD was also captured bound to a non-consensus site ATGGC even in the presence of its canonical site GAGGC. Our observations taken together with the known biochemical and structural features of the T-ag-origin interaction suggest a model for origin unwinding.

Selected figure(s)

Figure 4.
Figure 4 Structural details of T-ag interaction with DNA bases in the PEN-2 and PEN-4 structures. (A) Sequence-specific interaction of Arg 154 with G1 (the first G in the GAGGC pentamer) in the PEN-4 structure. A representative electron density map (shown in blue) is superimposed on the model. (B) Nonspecific interaction of Arg 154 with A1 (A in position of G1) in the PEN-2 structure. A representative electron density is superimposed on Arg 154. (C) Sequence-specific interaction of Ser 152 with A2. (D) Nonspecific interaction of Ser 152 with the T2 in the PEN-2 structure. Sequence-specific interactions, which involve (E) the G3 and Asn 153, (F) the G4 and Asn 153, and (G) the G (complementary to C5) with Arg 204. The protein and DNA are shown as stick models and colored by atom type; yellow for carbon, blue for nitrogen, red for oxygen, and purple for phosphorus. A representative electron density as captured from 2F[o]-F[c] map is shown with contours drawn at the 1.25 level. Hydrogen bonds are indicated with red dashed lines, and the length of the bonds is indicated in Å.

Figure 5.
Figure 5 Molecular model of an initial step in the SV40 DNA replication. The PEN-4 structure is shown in black, two hexameric helicase domains are in blue (PDB Id: 1N25), modeled DNA is shown as a stick model and colored per atom type (carbon in yellow, oxygen in red, nitrogen in blue, and phosphorus in purple). Position of the initially melted 8 nt fragment of EP with respect to the PEN box is highlighted with a yellow rectangle. Relative positions of the C-terminus in the OBD (aa 253) and N-terminus in the helicase domain (aa 266) are indicated. See text for more detail.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 5961-5969) copyright 2006.

Figures were selected by the author.