PDBsum entry 1vf9

DNA binding protein

PDB id: 1vf9

Contents

Protein chain

64 a.a. *

* Residue conservation analysis

PDB id:

1vf9

Name:

DNA binding protein

Title:

Solution structure of human trf2

Structure:

Telomeric repeat binding factor 2. Chain: a. Fragment: DNA binding domain. Synonym: ttaggg repeat binding factor 2, telomeric DNA binding protein. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

25 models

Authors:

Y.Nishimura,S.Hanaoka

Key ref:

S.Hanaoka et al. (2005). Comparison between TRF2 and TRF1 of their telomeric DNA-bound structures and DNA-binding activities. Protein Sci, 14, 119-130. PubMed id: 15608118 DOI: 10.1110/ps.04983705

Date:

12-Apr-04 Release date: 17-May-05

Protein chain

Q15554  (TERF2_HUMAN) -  Telomeric repeat-binding factor 2 from Homo sapiens

Seq: 542 a.a.

Struc: 64 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1110/ps.04983705

Protein Sci 14:119-130 (2005)

PubMed id: 15608118

Comparison between TRF2 and TRF1 of their telomeric DNA-bound structures and DNA-binding activities.

S.Hanaoka, A.Nagadoi, Y.Nishimura.

ABSTRACT

Mammalian telomeres consist of long tandem arrays of double-stranded telomeric TTAGGG repeats packaged by the telomeric DNA-binding proteins TRF1 and TRF2. Both contain a similar C-terminal Myb domain that mediates sequence-specific binding to telomeric DNA. In a DNA complex of TRF1, only the single Myb-like domain consisting of three helices can bind specifically to double-stranded telomeric DNA. TRF2 also binds to double-stranded telomeric DNA. Although the DNA binding mode of TRF2 is likely identical to that of TRF1, TRF2 plays an important role in the t-loop formation that protects the ends of telomeres. Here, to clarify the details of the double-stranded telomeric DNA-binding modes of TRF1 and TRF2, we determined the solution structure of the DNA-binding domain of human TRF2 bound to telomeric DNA; it consists of three helices, and like TRF1, the third helix recognizes TAGGG sequence in the major groove of DNA with the N-terminal arm locating in the minor groove. However, small but significant differences are observed; in contrast to the minor groove recognition of TRF1, in which an arginine residue recognizes the TT sequence, a lysine residue of TRF2 interacts with the TT part. We examined the telomeric DNA-binding activities of both DNA-binding domains of TRF1 and TRF2 and found that TRF1 binds more strongly than TRF2. Based on the structural differences of both domains, we created several mutants of the DNA-binding domain of TRF2 with stronger binding activities compared to the wild-type TRF2.

Selected figure(s)

Figure 4.
Figure 4. Comparison of DNA recognition modes between hTRF1 and hTRF2. (A) DNA recognition of the DNA-binding domain of hTRF2. The red circle indicates hydrophobic contact containing methyl groups of Ala484, Val485, and T3. Black broken lines indicate hydrophilic contacts between Asp489 and C7', C8'. (B) The interaction modes of Ser404/Ser417, Ala471/Ala484, and the phosphate group of T3. Black broken lines indicate hydrophilic contacts. (C) The interaction modes in the minor groove of DNA. Sidechains of Arg380 of hTRF1 and Lys447 of hTRF2, and DNA are shown. In hTRF1, the average distances over 20 structures between NH1 of Arg380 and O2 of T9, NH2 of Arg380 and O2 of T9, NH1 of Arg380 and N3 of A6', and NH2 of Arg380 and N3 of A6' are shown. In hTRF2, the average distances over 20 structures between NZ of Lys447 and O2 of T9, and NZ of Lys447 and N3 of A6' are shown. (D) The number of hydrogen bonds in the determined structures of the hTRF1 complex and the hTRF2 complex, respectively. The criteria of the hydrogen bonds were set as N-H o o D (O or N): N o o D distance < 3.5 Å; N-H-D angle > 90°.

Figure 5.
Figure 5. NMR titration experiments of the wild-type, K447R, A471S, A484S, R496K, DM (A471S/A484S), and QM (K447R/A471S/A484S/R496K) to the telomeric double-stranded DNA with the sequence GT-TAGGGTTAGGG.

The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 119-130) copyright 2005.

Figures were selected by an automated process.