3BBB

Crystal structure of the NM23-H2 transcription factor complex with dinucleotide d(AG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1.

Dexheimer, T.S.Carey, S.S.Zuohe, S.Gokhale, V.M.Hu, X.Murata, L.B.Maes, E.M.Weichsel, A.Sun, D.Meuillet, E.J.Montfort, W.R.Hurley, L.H.

(2009) Mol Cancer Ther 8: 1363-1377

  • DOI: 10.1158/1535-7163.MCT-08-1093
  • Primary Citation of Related Structures:  
    3BBC, 3BBF, 3BBB

  • PubMed Abstract: 
  • The formation of G-quadruplex structures within the nuclease hypersensitive element (NHE) III(1) region of the c-myc promoter and the ability of these structures to repress c-myc transcription have been well established. However, just how these extre ...

    The formation of G-quadruplex structures within the nuclease hypersensitive element (NHE) III(1) region of the c-myc promoter and the ability of these structures to repress c-myc transcription have been well established. However, just how these extremely stable DNA secondary structures are transformed to activate c-myc transcription is still unknown. NM23-H2/nucleoside diphosphate kinase B has been recognized as an activator of c-myc transcription via interactions with the NHE III(1) region of the c-myc gene promoter. Through the use of RNA interference, we confirmed the transcriptional regulatory role of NM23-H2. In addition, we find that further purification of NM23-H2 results in loss of the previously identified DNA strand cleavage activity, but retention of its DNA binding activity. NM23-H2 binds to both single-stranded guanine- and cytosine-rich strands of the c-myc NHE III(1) and, to a lesser extent, to a random single-stranded DNA template. However, it does not bind to or cleave the NHE III(1) in duplex form. Significantly, potassium ions and compounds that stabilize the G-quadruplex and i-motif structures have an inhibitory effect on NM23-H2 DNA-binding activity. Mutation of Arg(88) to Ala(88) (R88A) reduced both DNA and nucleotide binding but had minimal effect on the NM23-H2 crystal structure. On the basis of these data and molecular modeling studies, we have proposed a stepwise trapping-out of the NHE III(1) region in a single-stranded form, thus allowing single-stranded transcription factors to bind and activate c-myc transcription. Furthermore, this model provides a rationale for how the stabilization of the G-quadruplex or i-motif structures formed within the c-myc gene promoter region can inhibit NM23-H2 from activating c-myc gene expression.


    Related Citations: 
    • X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution.
      Morera, S., Lacombe, M.L., Xu, Y., LeBras, G., Janin, J.
      (1995) Structure 3: 1307

    Organizational Affiliation

    College of Pharmacy,University of Arizona, Tucson, Arizona 85721, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase BABCDEF151Homo sapiensMutation(s): 0 
Gene Names: NME2NM23B
EC: 2.7.4.6 (PDB Primary Data), 2.7.13.3 (UniProt)
Find proteins for P22392 (Homo sapiens)
Explore P22392 
Go to UniProtKB:  P22392
NIH Common Fund Data Resources
PHAROS  P22392
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DG
Query on DG

Download CCD File 
B, C, E, F
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
 Ligand Interaction
DA
Query on DA

Download CCD File 
C, E
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DAKd :  100   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.466α = 90
b = 118.219β = 90
c = 128.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDISPLAYFdata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance