PDBsum entry: 1bhn

Phosphotransferase

PDB id: 1bhn

Contents

Protein chains

(+ 0 more) 151 a.a. *

Ligands

35G-GDP ×6

Waters ×306

* Residue conservation analysis

PDB id:

1bhn

Name:

Phosphotransferase

Title:

Nucleoside diphosphate kinase isoform a from bovine retina

Structure:

Nucleoside diphosphate transferase. Chain: a, b, c, d, e, f. Engineered: yes

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: retina. Tissue: eye. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.40Å R-factor: 0.200

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:

J.E.Ladner et al. (1999). The three-dimensional structures of two isoforms of nucleoside diphosphate kinase from bovine retina. Acta Crystallogr D Biol Crystallogr, 55, 1127-1135. PubMed id: 10329774 DOI: 10.1107/S0907444999002528

Date:

10-Jun-98 Release date: 16-Feb-99

Protein chains

P52174  (NDKA1_BOVIN) -  Nucleoside diphosphate kinase A 1

Seq: 152 a.a.

Struc: 151 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.4.6 - Nucleoside-diphosphate kinase.
• Reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate

ATP + nucleoside diphosphate = ADP (Bound ligand (Het Group name = GDP) matches with 96.00% similarity) + nucleoside triphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (4 terms)
• Biological process: cell differentiation (7 terms)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1107/S0907444999002528

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

PubMed id: 10329774

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

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

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. 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.

Selected figure(s)

Figure 5.
Figure 5 The active site of NBR-B. The chain C residues near the active site are represented as space-filling models with radii 70% of the van der Waals radii. The cGMP molecule and chain A Glu152 are represented as stick models. This figure was generated using TkRaster3d (Bacon & Anderson, 1988[Bacon, D. J. & Anderson, W. F. (1988). J. Mol. Graph. 6, 219-220.]; Merritt & Murphy, 1994[Merritt, E. A. & Murphy, M. E. P. (1994). Acta Cryst. D50, 869-873.]).

Figure 7.
Figure 7 Superposition of monomers from NDP-kinases from other biological sources on the trimer from NBR-B. The figure was generated in TURBO FRODO (Roussel et al., 1996[Roussel, A., Inisan, A.-G. & Cambillau, C. (1996). TURBO FRODO. AFMB and BioGraphics, Marseille, France.]).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 1127-1135) copyright 1999.

Figures were selected by an automated process.