PDBsum entry: 1nsq

Phosphotransferase

PDB id: 1nsq

Contents

Protein chains

152 a.a. *

Waters ×257

* Residue conservation analysis

PDB id:

1nsq

Name:

Phosphotransferase

Title:

Mechanism of phosphate transfer by nucleoside diphosphate ki ray structures of a phospho-histidine intermediate of the e from drosophila and dictyostelium

Structure:

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

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227

Biol. unit:

Hexamer (from PQS)

Resolution:

2.18Å R-factor: 0.180

Authors:

J.Janin,M.Chiadmi,S.Morera,G.Lebras,I.Lascu

Key ref:

S.Moréra et al. (1995). Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium. Biochemistry, 34, 11062-11070. PubMed id: 7669763 DOI: 10.1021/bi00035a011

Date:

24-Apr-95 Release date: 10-Jul-95

Protein chains

P08879  (NDKA_DROME) -  Nucleoside diphosphate kinase

Seq: 153 a.a.

Struc: 152 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: cytoplasm (5 terms)
• Biological process: microtubule-based process (16 terms)
• Biochemical function: nucleotide binding (9 terms)

reference

DOI no: 10.1021/bi00035a011

Biochemistry 34:11062-11070 (1995)

PubMed id: 7669763

Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium.

S.Moréra, M.Chiadmi, G.LeBras, I.Lascu, J.Janin.

ABSTRACT

Nucleoside diphosphate kinase (NDP kinase) has a ping-pong mechanism with a phosphohistidine intermediate. Crystals of the enzymes from Dictyostelium discoideum and from Drosophila melanogaster were treated with phosphoramidate, and their X-ray structures were determined at 2.1 and 2.2 A resolution, respectively. The atomic models, refined to R factors below 20%, show no conformation change relative to the free proteins. In both enzymes, the active site histidine was phosphorylated on N delta, and it was the only site of phosphorylation. The phosphate group interacts with the hydroxyl group of Tyr56 and with protein-bound water molecules. Its environment is compared with that of phosphohistidines in succinyl-CoA synthetase and in phosphocarrier proteins. The X-ray structures of phosphorylated NDP kinase and of previously determined complexes with nucleoside diphosphates provide a basis for modeling the Michaelis complex with a nucleoside triphosphate, that of the phosphorylated protein with a nucleoside diphosphate, and the transition state of the phosphate transfer reaction in which the gamma-phosphate is pentacoordinated.