PDBsum entry: 1hhq

Transferase

PDB id: 1hhq

Contents

Protein chain

150 a.a. *

Ligands

SO4

Waters ×134

* Residue conservation analysis

PDB id:

1hhq

Name:

Transferase

Title:

Role of active site resiude lys16 in nucleoside diphosphate kinase

Structure:

Nucleoside diphosphate kinase. Chain: a. Engineered: yes. Mutation: yes. Other_details: ammounium sulfate

Source:

Dictyostelium discoideum. Organism_taxid: 44689. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.1Å R-factor: 0.177 R-free: 0.255

Authors:

B.Schneider,M.Babolat,Y.W.Xu,J.Janin,M.Veron,D.Deville-Bonne

Key ref:

B.Schneider et al. (2001). Mechanism of phosphoryl transfer by nucleoside diphosphate kinase pH dependence and role of the active site Lys16 and Tyr56 residues. Eur J Biochem, 268, 1964-1971. PubMed id: 11277918 DOI: 10.1046/j.1432-1327.2001.02070.x

Date:

26-Dec-00 Release date: 31-May-01

Protein chain

P22887  (NDKC_DICDI) -  Nucleoside diphosphate kinase, cytosolic

Seq: 155 a.a.

Struc: 150 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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 

• Cellular component: plasma membrane (6 terms)
• Biological process: cytoskeleton organization (11 terms)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1046/j.1432-1327.2001.02070.x

Eur J Biochem 268:1964-1971 (2001)

PubMed id: 11277918

Mechanism of phosphoryl transfer by nucleoside diphosphate kinase pH dependence and role of the active site Lys16 and Tyr56 residues.

B.Schneider, M.Babolat, Y.W.Xu, J.Janin, M.Véron, D.Deville-Bonne.

ABSTRACT

Nucleoside diphosphate (NDP) kinase phosphorylates nucleoside diphosphates with little specificity for the base and the sugar. Although nucleotide analogues used in antiviral therapies are also metabolized to their triphosphate form by NDP kinase, their lack of the 3'-hydroxyl of the ribose, which allows them to be DNA chain terminators, severely impairs the catalytic efficiency of NDP kinase. We have analyzed the kinetics parameters of several mutant NDP kinases modified on residues (Lys16, Tyr56, Asn119) interacting with the gamma-phosphate and/or the 3'-OH of the Mg2+-ATP substrate. We compared the relative contributions of the active-site residues and the substrate 3'-OH for point mutations on Lys16, Tyr56 and Asn119. Analysis of additional data from pH profiles identify the ionization state of these residues in the enzyme active form. X-ray structure of K16A mutant NDP kinase shows no detectable rearrangement of the residues of the active site.

Selected figure(s)

Figure 1.
Fig. 1. Stucture of the active site of mutant and wild-type NDP kinase. (A) Structure of the active site of K16A mutant NDP kinase from Dictyostelium (1HHQ.pdb coordinates). (B) Active site of NDP kinase from Dictyostelium with bound ADP-AlF[3] showing the pyrophosphate moiety of ADP, the bound Mg^2+ and surrounding protein side chains. Dash lines indicate the atoms at H-bond distances (1KDN.pdb coordinates).

Figure 2.
Fig. 2. pH dependence of the velocity of NDP kinase. (A) ( ) wild-type (B) ( ) Y56A, (C) (•) K16R and (D) ( ) K16A. NDP kinase activity is measured in AMT buffer in ‘standard’ substrate conditions ([ATP] = 1 m M, [dTDP] = 0.2 m M). The measured rates correspond to the value of k[cat] multiplied by a factor of 0.7.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2001, 268, 1964-1971) copyright 2001.

Figures were selected by an automated process.