1BE4

NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM B FROM BOVINE RETINA


Experimental Data Snapshot

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

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Nucleoside diphosphate kinase from bovine retina: purification, subcellular localization, molecular cloning, and three-dimensional structure.

Abdulaev, N.G.Karaschuk, G.N.Ladner, J.E.Kakuev, D.L.Yakhyaev, A.V.Tordova, M.Gaidarov, I.O.Popov, V.I.Fujiwara, J.H.Chinchilla, D.Eisenstein, E.Gilliland, G.L.Ridge, K.D.

(1998) Biochemistry 37: 13958-13967

  • DOI: https://doi.org/10.1021/bi980853s
  • Primary Citation of Related Structures:  
    1BE4

  • PubMed Abstract: 

    The biochemical and structural properties of bovine retinal nucleoside diphosphate kinase were investigated. The enzyme showed two polypeptides of approximately 17.5 and 18.5 kDa on SDS-PAGE, while isoelectric focusing revealed seven to eight proteins with a pI range of 7.4-8.2. Sedimentation equilibrium yielded a molecular mass of 96 +/- 2 kDa for the enzyme. Carbohydrate analysis revealed that both polypeptides contained Gal, Man, GlcNAc, Fuc, and GalNac saccharides. Like other nucleoside diphosphate kinases, the retinal enzyme showed substantial differences in the Km values for various di- and triphosphate nucleotides. Immunogold labeling of bovine retina revealed that the enzyme is localized on both the membranes and in the cytoplasm. Screening of a retinal cDNA library yielded full-length clones encoding two distinct isoforms (NBR-A and NBR-B). Both isoforms were overexpressed in Escherichia coli and their biochemical properties compared with retinal NDP-kinase. The structures of NBR-A and NBR-B were determined by X-ray crystallography in the presence of guanine nucleotide(s). Both isoforms are hexameric, and the fold of the monomer is similar to other nucleoside diphosphate kinase structures. The NBR-A active site contained both a cGMP and a GDP molecule each bound at half occupancy while the NBR-B active site contained only cGMP.


  • Organizational Affiliation

    Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, University of Maryland Biotechnology Institute, Rockville 20850, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEOSIDE DIPHOSPHATE TRANSFERASE
A, B, C
151Bos taurusMutation(s): 0 
EC: 2.7.4.6
UniProt
Find proteins for P52175 (Bos taurus)
Explore P52175 
Go to UniProtKB:  P52175
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52175
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.61α = 90
b = 128.61β = 90
c = 88.18γ = 90
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement
XENGENdata reduction
XENGENdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2023-08-02
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-05-22
    Changes: Data collection