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PDBsum entry 2kdz

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protein dna_rna links
Transcription/DNA PDB id
2kdz
Jmol
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'-
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q58HP2  (Q58HP2_TRIVA) -  MYB24
Seq:
Struc:
206 a.a.
107 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     chromatin binding     2 terms  

 

 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20565873 C.C.Chou, M.Rajasekaran, and C.Chen (2010).
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking.
  BMC Bioinformatics, 11, 334.  
20204171 C.Gomez, M.Esther Ramirez, M.Calixto-Galvez, O.Medel, and M.A.Rodríguez (2010).
Regulation of gene expression in protozoa parasites.
  J Biomed Biotechnol, 2010, 726045.  
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