PDBsum entry 2kdz

Transcription/DNA

PDB id: 2kdz

Contents

Protein chain

107 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

2kdz

Name:

Transcription/DNA

Title:

Structure of the r2r3 DNA binding domain of myb1 protein from protozoan parasite trichomonas vaginalis in complex with mre-1/mre-2r DNA

Structure:

Myb24. Chain: a. Fragment: myb1 r2r3 domain. Engineered: yes. 5'-d( Ap Ap Gp Ap Tp Ap Ap Cp Gp Ap Tp Ap Tp Tp Tp A)-3'. Chain: b. Engineered: yes. 5'-d( Tp Ap Ap Ap Tp Ap Tp Cp Gp Tp Tp Ap Tp Cp Tp T)-3'. Chain: c.

Source:

Trichomonas vaginalis. Organism_taxid: 5722. Strain: t1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

NMR struc:

10 models

Authors:

Y.C.Lou,S.Y.Wei,M.Rajasekaran,C.C.Chou,H.M.Hsu,J.H.Tai,C.Chen

Key ref:

Y.C.Lou et al. (2009). NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis. Nucleic Acids Res, 37, 2381-2394. PubMed id: 19246540

Date:

21-Jan-09 Release date: 17-Mar-09

Protein chain

Q58HP2  (Q58HP2_TRIVA) -  MYB24 from Trichomonas vaginalis

Seq: 206 a.a.

Struc: 107 a.a.

DNA/RNA chains

A-A-G-A-T-A-A-C-G-A-T-A-T-T-T-A 16 bases

T-A-A-A-T-A-T-C-G-T-T-A-T-C-T-T 16 bases

Enzyme reactions

• Enzyme class: E.C.?

Nucleic Acids Res 37:2381-2394 (2009)

PubMed id: 19246540

NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis.

Y.C.Lou, S.Y.Wei, M.Rajasekaran, C.C.Chou, H.M.Hsu, J.H.Tai, C.Chen.

ABSTRACT

The transcription regulator, tvMyb1, is the first Myb family protein identified in Trichomonas vaginalis. Using an electrophoretic mobility shift assay, we defined the amino-acid sequence from Lys(35) to Ser(141) (tvMyb1(35-141)) as the minimal DNA-binding domain, encompassing two Myb-like DNA-binding motifs (designated as R2 and R3 motifs) and an extension of 10 residues at the C-terminus. NMR solution structures of tvMyb1(35-141) show that both the R2 and R3 motifs adopt helix-turn-helix conformations while helix 6 in the R3 motif is longer than its counterpart in vertebrate Myb proteins. The extension of helix 6 was then shown to play an important role in protein stability as well as in DNA-binding activity. The structural basis for the tvMyb1(35-141)/DNA interaction was investigated using chemical shift perturbations, residual dipolar couplings, DNA specificity data and data-driven macromolecular docking by HADDOCK. Our data indicate that the orientation between R2 and R3 motifs dramatically changes upon binding to DNA so as to recognize the DNA major groove through a number of key contacts involving residues in helices 3 and 6. The tvMyb1(35-141)/DNA complex model furthers our understanding of DNA recognition by Myb proteins and this approach could be applied in determining the complex structures involving proteins with multiple domains.