2OKV

c-Myc DNA Unwinding Element Binding Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Function of the c-myc DNA-unwinding Element-binding Protein DUE-B.

Kemp, M.Bae, B.Yu, J.P.Ghosh, M.Leffak, M.Nair, S.K.

(2007) J.Biol.Chem. 282: 10441-10448

  • DOI: 10.1074/jbc.M609632200

  • PubMed Abstract: 
  • Local zones of easily unwound DNA are characteristic of prokaryotic and eukaryotic replication origins. The DNA-unwinding element of the human c-myc replication origin is essential for replicator activity and is a target of the DNA-unwinding element- ...

    Local zones of easily unwound DNA are characteristic of prokaryotic and eukaryotic replication origins. The DNA-unwinding element of the human c-myc replication origin is essential for replicator activity and is a target of the DNA-unwinding element-binding protein DUE-B in vivo. We present here the 2.0A crystal structure of DUE-B and complementary biochemical characterization of its biological activity. The structure corresponds to a dimer of the N-terminal domain of the full-length protein and contains many of the structural elements of the nucleotide binding fold. A single magnesium ion resides in the putative active site cavity, which could serve to facilitate ATP hydrolytic activity of this protein. The structure also demonstrates a notable similarity to those of tRNA-editing enzymes. Consistent with this structural homology, the N-terminal core of DUE-B is shown to display both D-aminoacyl-tRNA deacylase activity and ATPase activity. We further demonstrate that the C-terminal portion of the enzyme is disordered and not essential for dimerization. However, this region is essential for DNA binding in vitro and becomes ordered in the presence of DNA.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable D-tyrosyl-tRNA(Tyr) deacylase 1
A, B, C, D
209Homo sapiensGene Names: DTD1 (C20orf88, DUEB, HARS2)
EC: 3.1.-.-
Find proteins for Q8TEA8 (Homo sapiens)
Go to Gene View: DTD1
Go to UniProtKB:  Q8TEA8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 77.813α = 90.00
b = 77.813β = 90.00
c = 106.423γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
HKL-2000data scaling
HKL-2000data reduction
ADSCdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-01-17 
  • Released Date: 2007-01-30 
  • Deposition Author(s): Bae, B., Nair, S.K.

Revision History 

  • Version 1.0: 2007-01-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance