PDBsum entry 1jb7

DNA-binding protein/DNA

PDB id: 1jb7

Contents

Protein chains

460 a.a. *

216 a.a. *

DNA/RNA

Metals

_NA ×4

_CL

Waters ×503

* Residue conservation analysis

PDB id:

1jb7

Name:

DNA-binding protein/DNA

Title:

DNA g-quartets in a 1.86 a resolution structure of an oxytricha nova telomeric protein-DNA complex

Structure:

5'-d( Gp Gp Gp Gp Tp Tp Tp Tp Gp Gp Gp G)-3'. Chain: d, g, h. Engineered: yes. Other_details: chain d is single strand DNA. Chains g and h are a g- quartet linked DNA dimer. Telomere-binding protein alpha subunit. Chain: a. Engineered: yes. Other_details: alanine version.

Source:

Synthetic: yes. Other_details: 3' terminal single strand DNA sequence of macronuclear telomeres. Sterkiella nova. Organism_taxid: 200597. Gene: mac-56a. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: mac-41a.

Biol. unit:

Pentamer (from PQS)

Resolution:

1.86Å R-factor: 0.230 R-free: 0.246

Authors:

M.P.Horvath,S.C.Schultz

Key ref:

M.P.Horvath and S.C.Schultz (2001). DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex. J Mol Biol, 310, 367-377. PubMed id: 11428895 DOI: 10.1006/jmbi.2001.4766

Date:

02-Jun-01 Release date: 11-Jun-01

Protein chain

P29549  (TEBA_STENO) -  Telomere-binding protein subunit alpha from Sterkiella nova

Seq: 495 a.a.

Struc: 460 a.a.

Protein chain

P16458  (TEBB_STENO) -  Telomere-binding protein subunit beta from Sterkiella nova

Seq: 385 a.a.

Struc: 216 a.a.

DNA/RNA chains

G-G-G-G-T-T-T-T-G-G-G-G 12 bases

G-G-G-G-T-T-T-T-G-G-G-G 12 bases

G-G-G-G-T-T-T-T-G-G-G-G 12 bases

DOI no: 10.1006/jmbi.2001.4766

J Mol Biol 310:367-377 (2001)

PubMed id: 11428895

DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex.

M.P.Horvath, S.C.Schultz.

ABSTRACT

The Oxytricha nova telomere end binding protein (OnTEBP) recognizes, binds and protects the single-stranded 3'-terminal DNA extension found at the ends of macronuclear chromosomes. The structure of this complex shows that the single strand GGGGTTTTGGGG DNA binds in a deep cleft between the two protein subunits of OnTEBP, adopting a non-helical and irregular conformation. In extending the resolution limit of this structure to 1.86 A, we were surprised to find a G-quartet linked dimer of the GGGGTTTTGGGG DNA also packing within the crystal lattice and interacting with the telomere end binding protein. The G-quartet DNA exhibits the same structure and topology as previously observed in solution by NMR with diagonally crossing d(TTTT) loops at either end of the four-stranded helix. Additionally, the crystal structure reveals clearly visible Na(+), and specific patterns of bound water molecules in the four non-equivalent grooves. Although the G-quartet:protein contact surfaces are modest and might simply represent crystal packing interactions, it is interesting to speculate that the two types of telomeric DNA-protein interactions observed here might both be important in telomere biology.

Selected figure(s)

Figure 4.
Figure 4. Hydration of the G-quartet linked G[4]T[4]G[4] DNA dimer. Electron density maps and schematic representations are shown side-by-side for water molecules bound in the four grooves. The electron density map is colored gray for the DNA grooves and blue for the water molecules. In the schematic phosphorous atoms are colored yellow, non-bridging phosphate oxygen atoms are red, N2 (and N3 if shown) atoms are green, the C8 atom is gray, water molecules are cyan for 1–2 σ peaks in the S.A. omit electron density maps and dark blue for>2 σ peaks. The deoxyribose group is a pentagon and the bases are represented as rectangles. The position in the 5′ → 3′ sequence and the syn/anti conformation about the N-glycosyl bond of each base is indicated. From top to bottom the grooves are the (a) wide groove (10 Å across), (b) intermediate I (4.6 Å across), (c) narrow (3.0 Å across), and (d) intermediate II (4.6 Å across). The two intermediate grooves and associated hydration patterns are pseudo 2-fold symmetric, so each DNA-water interaction is corroborated by two independent observations. In solution, the wide and narrow grooves are each pseudo 2-fold symmetric, but water interactions are not exactly repeated in the top and bottom halves of these two grooves presumably because of protein and lattice interactions.

Figure 5.
Figure 5. Distribution of waters interacting with N3, N2, and C8 groups of the G bases. (a) All 16 G-G base-pairs are superimposed and shown as a generalized G-G pair. The number of observations for each hydration site is indicated. (b) The N2-water-O4' bridge and the C8-water-OP bridge are shown for the anti-anti G-G configuration. (c) The N2-water-OP bridge and (d) the C8-water-O4' bridge are other examples of bidentate water interactions and each of these bridges involves a base in the syn conformation.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 310, 367-377) copyright 2001.

Figures were selected by an automated process.