PDBsum entry: 1s57

Transferase

PDB id: 1s57

Contents

Protein chains

(+ 0 more) 153 a.a. *

Ligands

SO4 ×18

EPE ×6

Waters ×545

* Residue conservation analysis

PDB id:

1s57

Name:

Transferase

Title:

Crystal structure of nucleoside diphosphate kinase 2 from arabidopsis

Structure:

Nucleoside diphosphate kinase ii. Chain: a, b, c, d, e, f. Synonym: nucleoside diphosphate kinase 2, ndk ii, ndp kinase ii, ndpk ii, ndpk ia. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: ndpk2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PQS)

Resolution:

1.80Å R-factor: 0.212 R-free: 0.241

Authors:

Y.J.Im,J.-I.Kim,Y.Shen,Y.Na,Y.-J.Han,S.-H.Kim,P.-S.Song, S.H.Eom

Key ref:

Y.J.Im et al. (2004). Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling. J Mol Biol, 343, 659-670. PubMed id: 15465053 DOI: 10.1016/j.jmb.2004.08.054

Date:

20-Jan-04 Release date: 30-Nov-04

Protein chains

O64903  (NDK2_ARATH) -  Nucleoside diphosphate kinase II, chloroplastic

Seq: 231 a.a.

Struc: 153 a.a.

Enzyme reactions

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

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

 Gene Ontology (GO) functional annotation 

• Biological process: GTP biosynthetic process (3 terms)
• Biochemical function: nucleoside diphosphate kinase activity (2 terms)

reference

DOI no: 10.1016/j.jmb.2004.08.054

J Mol Biol 343:659-670 (2004)

PubMed id: 15465053

Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling.

Y.J.Im, J.I.Kim, Y.Shen, Y.Na, Y.J.Han, S.H.Kim, P.S.Song, S.H.Eom.

ABSTRACT

In plants, nucleoside diphosphate kinases (NDPKs) play a key role in the signaling of both stress and light. However, little is known about the structural elements involved in their function. Of the three NDPKs (NDPK1-NDPK3) expressed in Arabidopsis thaliana, NDPK2 is involved in phytochrome-mediated signal transduction. In this study, we found that the binding of dNDP or NTP to NDPK2 strengthens the interaction significantly between activated phytochrome and NDPK2. To better understand the structural basis of the phytochrome-NDPK2 interaction, we determined the X-ray structures of NDPK1, NDPK2, and dGTP-bound NDPK2 from A.thaliana at 1.8A, 2.6A, and 2.4A, respectively. The structures showed that nucleotide binding caused a slight conformational change in NDPK2 that was confined to helices alphaA and alpha2. This suggests that the presence of nucleotide in the active site and/or the evoked conformational change contributes to the recognition of NDPK2 by activated phytochrome. In vitro binding assays showed that only NDPK2 interacted specifically with the phytochrome and the C-terminal regulatory domain of phytochrome is involved in the interaction. A domain swap experiment between NDPK1 and NDPK2 showed that the variable C-terminal region of NDPK2 is important for the activation by phytochrome. The structure of Arabidopsis NDPK1 and NDPK2 showed that the isoforms share common electrostatic surfaces at the nucleotide-binding site, but the variable C-terminal regions have distinct electrostatic charge distributions. These findings suggest that the binding of nucleotide to NDPK2 plays a regulatory role in phytochrome signaling and that the C-terminal extension of NDPK2 provides a potential binding surface for the specific interaction with phytochromes.

Selected figure(s)

Figure 3.
Figure 3. The g-phosphate exchange activity of domain-swapped NDPK mutants. A, Domain structure of the domain-swap mutants between NDPK1 and NDPK2. In all, 45 residues in the C-terminal domain of both NDPKs were switched. Mutant NK21 contains the N-terminal domain of NDPK2 and the C-terminal domain of NDPK1, whereas mutant NK12 contains the N-terminal domain of NDPK1 and the C-terminal domain of NDPK2. B, The stimulation of the g-phosphate exchange activities of NDPK1 and NDPK2 by the Pfr form of oat phyA. Only NDPK2 is activated by phytochrome in a concentration-dependent manner. C, The stimulation of the g-phosphate exchange activities of domain swap mutants by the Pfr form of oat phyA. Mutant NK12, which contains the C-terminal domain of NDPK2, was stimulated by the Pfr form of oat phyA significantly, whereas mutant NK21 was little stimulated by the Pfr form of phyA.

Figure 4.
Figure 4. Structure of Arabidopsis thaliana NDPK2. A, Ribbon diagram of an NDPK2 hexamer viewed along the 3-fold axis. The hexamer rotated 90° perpendicular to the 3-fold axis is shown on the right. B, Ribbon diagram showing an NDPK2 monomer with a ball-and-stick model showing the bound dGTP. 2F[o] -F[c] map of the dGTP molecule is shown. C, Superposition of C^a traces of the apo and nucleotide-bound structures. The apo form is colored in wheat and the dGTP bound form in blue. The Figures were made using PyMOL (http://pymol.sourceforge.net). D, Illustration of amino-acid contacts to the dGTP ligand in the active site. Hydrogen bonds and salt-bridges are shown as broken green lines and van der Waals contacts as bent red combs. The Figure was produced using LIGPLOT.54

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 343, 659-670) copyright 2004.

Figures were selected by an automated process.