PDBsum entry: 1bux

Phosphotransferase

PDB id: 1bux

Contents

Protein chains

150 a.a. *

Ligands

PPS ×3

* Residue conservation analysis

PDB id:

1bux

Name:

Phosphotransferase

Title:

3'-phosphorylated nucleotides binding to nucleoside diphosphate kinase

Structure:

Nucleoside diphosphate kinase. Chain: a, b, c. Synonym: ndp kinase. Engineered: yes

Source:

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

Biol. unit:

Homo-Hexamer (from PDB file)

Resolution:

2.80Å R-factor: 0.204 R-free: 0.312

Authors:

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

Key ref:

B.Schneider et al. (1998). 3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity. J Biol Chem, 273, 28773-28778. PubMed id: 9786875 DOI: 10.1074/jbc.273.44.28773

Date:

07-Sep-98 Release date: 27-Apr-99

Protein chains

P22887  (NDKC_DICDI) -  Nucleoside diphosphate kinase, cytosolic

Seq: 155 a.a.

Struc: 150 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 = PPS) matches with 65.00% similarity) + 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: 10.1074/jbc.273.44.28773

J Biol Chem 273:28773-28778 (1998)

PubMed id: 9786875

3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity.

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

ABSTRACT

Nucleoside diphosphate (NDP) kinase catalyzes the phosphorylation of ribo- and deoxyribonucleosides diphosphates into triphosphates. NDP kinase is also involved in malignant tumors and was shown to activate in vitro transcription of the c-myc oncogene by binding to its NHE sequence. The structure of the complex of NDP kinase with bound ADP shows that the nucleotide adopts a different conformation from that observed in other phosphokinases with an internal H bond between the 3'-OH and the beta-O made free by the phosphate transfer. We use intrinsic protein fluorescence to investigate the inhibitory and binding potential of nucleotide analogues phosphorylated in 3'-OH position of the ribose to both wild type and F64W mutant NDP kinase from Dictyostelium discoideum. Due to their 3'-phosphate, 5'-phosphoadenosine 3'-phosphate (PAP) and adenosine 3'-phosphate 5'-phosphosulfate (PAPS) can be regarded as structural analogues of enzyme-bound ADP. The KD of PAPS (10 microM) is three times lower than the KD of ADP. PAPS also acts as a competitive inhibitor toward natural substrates during catalysis, with a KI in agreement with binding data. The crystal structure of the binary complex between Dictyostelium NDP kinase and PAPS was solved at 2.8-A resolution. It shows a new mode of nucleotide binding at the active site with the 3'-phosphate of PAPS located near the catalytic histidine, at the same position as the gamma-phosphate in the transition state. The sulfate group is directed toward the protein surface. PAPS will be useful for the design of high affinity drugs targeted to NDP kinases.

Selected figure(s)

Figure 5.
Fig. 5. PAPS binding to the protein. A, PAPS (ball-and-sticks) in the active site of subunit A. Protein is shown with a thin line as a C trace. The side chains of His122, Phe^64, and Val116 are explicitly drawn. All substrates bind to NDP kinase at the same site. B, detail of interactions between PAPS and the protein binding site. Key residues are labeled. The adenine base of PAPS points down and the 3'-phosphate group up toward His122. Dashed lines indicate polar interactions. Empty bonds indicate alternative conformations of the sulfate group.

Figure 6.
Fig. 6. Comparison of PAPS with ADP-AlF[3] (A) and PAP with cAMP (B) in the active site of NDP kinases. PAPS-PAP and protein are shown in ball-and-sticks. ADP-AlF[3] and cAMP are shown by black lines. Dashes indicate polar interactions. The ADP-AlF[3] complex (37) and cAMP complex (27) are superimposed by overlapping corresponding C atoms. PAPS is shown in one of the alternative conformations. Note that the 3'-phosphate of PAPS and the single phosphate of cAMP are near the position of AlF[3], which mimics the -phosphate transfer between NTP and His122.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 28773-28778) copyright 1998.

Figures were selected by an automated process.