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Phosphotransferase PDB id
1be4
Jmol
Contents
Protein chains
151 a.a. *
Ligands
PCG ×3
Waters ×278
* Residue conservation analysis
PDB id:
1be4
Name: Phosphotransferase
Title: Nucleoside diphosphate kinase isoform b from bovine retina
Structure: Nucleoside diphosphate transferase. Chain: a, b, c. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: eye. Tissue: retina. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PDB file)
Resolution:
2.40Å     R-factor:   0.198    
Authors: J.E.Ladner,N.G.Abdulaev,D.L.Kakuev,G.N.Karaschuk,M.Tordova, E.Eisenstein,J.H.Fujiwara,K.D.Ridge,G.L.Gilliland
Key ref:
N.G.Abdulaev et al. (1998). Nucleoside diphosphate kinase from bovine retina: purification, subcellular localization, molecular cloning, and three-dimensional structure. Biochemistry, 37, 13958-13967. PubMed id: 9760230 DOI: 10.1021/bi980853s
Date:
19-May-98     Release date:   13-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P52175  (NDKA2_BOVIN) -  Nucleoside diphosphate kinase A 2
Seq:
Struc: 		152 a.a.
151 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.4.6  - Nucleoside-diphosphate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
ATP
 + nucleoside diphosphate
 =
ADP
Bound ligand (Het Group name = PCG)
matches with 78.57% similarity 		+ nucleoside triphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     cell differentiation   9 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi980853s Biochemistry 37:13958-13967 (1998)
PubMed id: 9760230  
 
 
Nucleoside diphosphate kinase from bovine retina: purification, subcellular localization, molecular cloning, and three-dimensional structure.
N.G.Abdulaev, G.N.Karaschuk, J.E.Ladner, D.L.Kakuev, A.V.Yakhyaev, M.Tordova, I.O.Gaidarov, V.I.Popov, J.H.Fujiwara, D.Chinchilla, E.Eisenstein, G.L.Gilliland, K.D.Ridge.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19852809 T.Desvignes, P.Pontarotti, C.Fauvel, and J.Bobe (2009).
Nme protein family evolutionary history, a vertebrate perspective.
  BMC Evol Biol, 9, 256.  
17140383 Y.Mao, A.Deng, N.Qu, and X.Wu (2006).
ATPase domain of Hsp70 exhibits intrinsic ATP-ADP exchange activity.
  Biochemistry (Mosc), 71, 1222-1229.  
12486123 F.Cuello, R.A.Schulze, F.Heemeyer, H.E.Meyer, S.Lutz, K.H.Jakobs, F.Niroomand, and T.Wieland (2003).
Activation of heterotrimeric G proteins by a high energy phosphate transfer via nucleoside diphosphate kinase (NDPK) B and Gbeta subunits. Complex formation of NDPK B with Gbeta gamma dimers and phosphorylation of His-266 IN Gbeta.
  J Biol Chem, 278, 7220-7226.  
13678959 K.D.Ridge, N.G.Abdulaev, M.Sousa, and K.Palczewski (2003).
Phototransduction: crystal clear.
  Trends Biochem Sci, 28, 479-487.  
14665452 X.Lin, C.Momany, and M.Momany (2003).
SwoHp, a nucleoside diphosphate kinase, is essential in Aspergillus nidulans.
  Eukaryot Cell, 2, 1169-1177.  
11053861 K.Min, H.K.Song, C.Chang, J.Y.Lee, S.H.Eom, K.K.Kim, Y.G.Yu, and S.W.Suh (2000).
Nucleoside diphosphate kinase from the hyperthermophilic archaeon Methanococcus jannaschii: overexpression, crystallization and preliminary X-ray crystallographic analysis.
  Acta Crystallogr D Biol Crystallogr, 56, 1485-1487.  
10329774 J.E.Ladner, N.G.Abdulaev, D.L.Kakuev, M.Tordová, K.D.Ridge, and G.L.Gilliland (1999).
The three-dimensional structures of two isoforms of nucleoside diphosphate kinase from bovine retina.
  Acta Crystallogr D Biol Crystallogr, 55, 1127-1135.
PDB code: 1bhn
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