PDBsum entry: 1lwx

Phosphotransferase

PDB id: 1lwx

Contents

Protein chains

150 a.a. *

Ligands

AZD ×3

Metals

_MG ×2

Waters ×140

* Residue conservation analysis

PDB id:

1lwx

Name:

Phosphotransferase

Title:

Azt diphosphate binding to nucleoside diphosphate kinase

Structure:

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

Source:

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

Biol. unit:

Hexamer (from PQS)

Resolution:

2.30Å R-factor: 0.216 R-free: 0.280

Authors:

J.Janin,Y.Xu

Key ref:

Y.Xu et al. (1997). X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase. Proc Natl Acad Sci U S A, 94, 7162-7165. PubMed id: 9207061 DOI: 10.1073/pnas.94.14.7162

Date:

30-Apr-97 Release date: 20-Aug-97

Protein chains

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

ATP + nucleoside diphosphate = ADP (Bound ligand (Het Group name = AZD) matches with 63.64% 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 (13 terms)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1073/pnas.94.14.7162

Proc Natl Acad Sci U S A 94:7162-7165 (1997)

PubMed id: 9207061

X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase.

Y.Xu, O.Sellam, S.Moréra, S.Sarfati, R.Biondi, M.Véron, J.Janin.

ABSTRACT

To be effective as antiviral agent, AZT (3'-azido-3'-deoxythymidine) must be converted to a triphosphate derivative by cellular kinases. The conversion is inefficient and, to understand why AZT diphosphate is a poor substrate of nucleoside diphosphate (NDP) kinase, we determined a 2.3-A x-ray structure of a complex with the N119A point mutant of Dictyostelium NDP kinase. It shows that the analog binds at the same site and, except for the sugar ring pucker which is different, binds in the same way as the natural substrate thymidine diphosphate. However, the azido group that replaces the 3'OH of the deoxyribose in AZT displaces a lysine side chain involved in catalysis. Moreover, it is unable to make an internal hydrogen bond to the oxygen bridging the beta- and gamma-phosphate, which plays an important part in phosphate transfer.

Selected figure(s)

Figure 1.
Fig. 1. Stereoview of the superimposed AZT-DP and TDP structures at the NDP kinase active site. The N119A-AZT-DP complex is colored^ by atom type; the wild-type-dTDP complex (5) has white bonds. The electron density for AZT-DP is contoured at 3 in a 2.3 Å F[o] F[c] map. The thymine base points down toward outside the protein. The phosphates carry a Mg2+ ion (orange ball) and point toward the active site His-122 on top. Though the N119A mutation locally affects the main chain conformation, the protein structure is essentially the same in the two complexes and crowding by the 3 -azido group of AZT-DP is chiefly responsible for the observed movement of the Lys 16^ side chain. Drawn with TURBO (A. Roussel and C. Cambillau, Marseille, France, personal communication).

Figure 2.
Fig. 2. NDP kinase interactions with AZT-DP. The N3 azido group in the center is in contact with the side chains of Lys-16, of Ala-119^ replacing an asparagine in wild-type NDP kinase, and of His-122^ on top. It may also hydrogen bond to Arg 109. The grey ball is a Mg2+ ion interacting with both phosphate groups. The stereopair was drawn with MOLSCRIPT (16).