PDBsum entry: 1leo

Transferase

PDB id: 1leo

Contents

Protein chain

150 a.a. *

Waters ×20

* Residue conservation analysis

PDB id:

1leo

Name:

Transferase

Title:

P100s nucleoside diphosphate kinase

Structure:

Nucleoside diphosphate kinase. Chain: a. Synonym: ndp kinase. Engineered: yes. Mutation: yes

Source:

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

Biol. unit:

Hexamer (from PQS)

Resolution:

2.60Å R-factor: 0.193

Authors:

J.Janin,Y.Xu,M.Veron

Key ref:

A.Karlsson et al. (1996). Nucleoside diphosphate kinase. Investigation of the intersubunit contacts by site-directed mutagenesis and crystallography. J Biol Chem, 271, 19928-19934. PubMed id: 8702707 DOI: 10.1074/jbc.271.33.19928

Date:

22-May-96 Release date: 08-Nov-96

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 (13 terms)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1074/jbc.271.33.19928

J Biol Chem 271:19928-19934 (1996)

PubMed id: 8702707

Nucleoside diphosphate kinase. Investigation of the intersubunit contacts by site-directed mutagenesis and crystallography.

A.Karlsson, S.Mesnildrey, Y.Xu, S.Moréra, J.Janin, M.Véron.

ABSTRACT

NDP kinase from Dictyostelium was mutated by site-directed mutagenesis at positions indicated by structural data to be involved in the trimer interface. The mutants were substitutions at residue Pro-100 (P100S and P100G) and deletions of 1-5 residues at the C terminus. Single mutants yielded proteins that kept both activity and hexameric structure. However, they were severely affected in their stability toward temperature and urea denaturation. When the P100S mutation was combined with any of the C-terminal deletions, the enzyme lost most of its activity and dissociated into dimers. Crystallographic analysis of the P100S protein was performed at 2.6 A resolution. The x-ray structure showed no direct alteration of intersubunits contacts at residue 100, but an induced disruption of the interaction between Asp-115 and the C terminus of another subunit. The substitution of proline 100 to serine corresponds to the Killer-of-prune mutation in Drosophila. Consequences of the mutation are discussed in view of the structural and biochemical properties observed in the mutant Dictyostelium protein.

Selected figure(s)

Figure 2.
Fig. 2. The trimer interface in Dictyostelium NDP kinase. The trimer is viewed along the 3-fold axis. The box is detailed in the bottom panel. Contacts involve the Kpn-loop (residue 100-118) from the three monomers. Three contact regions are labeled A, B, and C. Region A involves residue Pro-105 from each Kpn-loop; region B, Pro-100; and residues 110-113 on one side, Lys-35 of helix [1] on the other; region C, Asp-115 on one side, the C-terminal Glu-155 on the other. Adapted from Moréra et al. (13).

Figure 7.
Fig. 7. Electron density for the Ser-100 side chain. The 2Fo-Fc map is contoured at 1 . Drawn with TURBO (A. Roussel & C. Cabillau, Marseille, France). The dotted line between D115 and P100S represents the H bond.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1996, 271, 19928-19934) copyright 1996.

Figures were selected by an automated process.