2OKV

c-Myc DNA Unwinding Element Binding Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

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
  • Primary Citation of Related Structures:  
    2OKV

  • 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-binding protein DUE-B in vivo ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable D-tyrosyl-tRNA(Tyr) deacylase 1A, B, C, D209Homo sapiensMutation(s): 0 
Gene Names: HARS2C20orf88DTD1DUEB
EC: 3.1 (PDB Primary Data), 3.1.1.96 (UniProt)
Find proteins for Q8TEA8 (Homo sapiens)
Explore Q8TEA8 
Go to UniProtKB:  Q8TEA8
NIH Common Fund Data Resources
PHAROS:  Q8TEA8
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.813α = 90
b = 77.813β = 90
c = 106.423γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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