1BHN

NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM A FROM BOVINE RETINA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å

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This is version 1.3 of the entry. See complete history


Literature

The three-dimensional structures of two isoforms of nucleoside diphosphate kinase from bovine retina.

Ladner, J.E.Abdulaev, N.G.Kakuev, D.L.Tordova, M.Ridge, K.D.Gilliland, G.L.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1127-1135

  • DOI: 10.1107/s0907444999002528
  • Primary Citation of Related Structures:  
    1BHN

  • PubMed Abstract: 
  • The crystal structures of two isoforms of nucleoside diphosphate kinase from bovine retina overexpressed in Escherischia coli have been determined to 2.4 A resolution. Both the isoforms, NBR-A and NBR-B, are hexameric and the fold of the monomer is in agreement with NDP-kinase structures from other biological sources ...

    The crystal structures of two isoforms of nucleoside diphosphate kinase from bovine retina overexpressed in Escherischia coli have been determined to 2.4 A resolution. Both the isoforms, NBR-A and NBR-B, are hexameric and the fold of the monomer is in agreement with NDP-kinase structures from other biological sources. Although the polypeptide chains of the two isoforms differ by only two residues, they crystallize in different space groups. NBR-A crystallizes in space group P212121 with an entire hexamer in the asymmetric unit, while NBR-B crystallizes in space group P43212 with a trimer in the asymmetric unit. The highly conserved nucleotide-binding site observed in other nucleoside diphosphate kinase structures is also observed here. Both NBR-A and NBR-B were crystallized in the presence of cGMP. The nucleotide is bound with the base in the anti conformation. The NBR-A active site contained both cGMP and GDP each bound at half occupancy. Presumably, NBR-A had retained GDP (or GTP) from the purification process. The NBR-B active site contained only cGMP.


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, National Institute of Standards and Technology and the University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850 USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEOSIDE DIPHOSPHATE TRANSFERASE
A, B, C, D, E, F
A, B, C, D, E, F
152Bos taurusMutation(s): 0 
Gene Names: NME1-1
EC: 2.7.4.6
UniProt
Find proteins for P52174 (Bos taurus)
Explore P52174 
Go to UniProtKB:  P52174
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52174
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.88α = 90
b = 92.11β = 90
c = 131.63γ = 90
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement
XENGENdata reduction
XENGENdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection