1NSK

THE CRYSTAL STRUCTURE OF A HUMAN NUCLEOSIDE DIPHOSPHATE KINASE, NM23-H2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of a human nucleoside diphosphate kinase, NM23-H2.

Webb, P.A.Perisic, O.Mendola, C.E.Backer, J.M.Williams, R.L.

(1995) J.Mol.Biol. 251: 574-587


  • PubMed Abstract: 
  • The 2.8 A resolution X-ray structure of NM23-H2 has been determined by molecular replacement using the structure of Myxococcus xanthus nucleoside diphosphate (NDP) kinase. NM23-H2 is a human NDP kinase. The enzyme catalyses phosphoryl transfer, binds ...

    The 2.8 A resolution X-ray structure of NM23-H2 has been determined by molecular replacement using the structure of Myxococcus xanthus nucleoside diphosphate (NDP) kinase. NM23-H2 is a human NDP kinase. The enzyme catalyses phosphoryl transfer, binds DNA, and can activate the transcription of the c-myc oncogene in vitro. NM23 has also been reported to be a suppressor of metastasis in some types of tumours. Whereas the M. xanthus NDP kinase is a tetramer, NM23-H2 is a hexamer. The fold of NM23-H2 is identical to the fold of other NDP kinases. Two antiparallel helices joined by a turn form one edge of the nucleotide binding cleft. This region moves in a hinge-like fashion in response to substrate binding and crystal packing forces. Additional differences in conformation among the NDP kinases are principally in regions involved in protein-protein contacts within the oligomers. The only protein-protein interaction conserved among all NDP kinases is a dimeric interaction. Several mutations of NM23-H2 have been detected in tumour tissues. These mutations do not involve residues interacting with the substrates, and probably destabilise the enzyme without directly affecting the catalytic activity. Low level phosphorylation of serines has been reported for NM23 both in vitro and in vivo. The structure of the hexamer indicates that two serine residues that have been reported as being phosphorylated, Ser44 and Ser122, are on the surface of the hexamer, and are likely to be phosphorylated by exogenous kinases. In contrast, Ser120 is buried, and is most likely phosphorylated by a direct transfer from the phosphohistidine intermediate of the reaction mechanism.


    Organizational Affiliation

    Centre for Protein Engineering, MRC Centre, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE DIPHOSPHATE KINASE
R, L, T, U, N, O
152Homo sapiensMutation(s): 0 
Gene Names: NME2 (NM23B)
EC: 2.7.4.6
Find proteins for P22392 (Homo sapiens)
Go to Gene View: NME2
Go to UniProtKB:  P22392
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 118.670α = 90.00
b = 118.800β = 90.00
c = 90.190γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance