PDBsum entry: 1nue

Phosphotransferase

PDB id: 1nue

Contents

Protein chains

(+ 0 more) 151 a.a. *

Ligands

GDP ×6

Metals

_MG ×2

Waters ×334

* Residue conservation analysis

PDB id:

1nue

Name:

Phosphotransferase

Title:

X-ray structure of nm23 human nucleoside diphosphate kinase b complexed with gdp at 2 angstroms resolution

Structure:

Nucleoside diphosphate kinase. Chain: a, b, c, d, e, f. Ec: 2.7.4.6

Source:

Homo sapiens. Human. Organism_taxid: 9606

Biol. unit:

Hexamer (from PQS)

Resolution:

2.00Å R-factor: 0.177

Authors:

S.Morera,M.-L.Lacombe,X.Yingwu,G.Lebras,J.Janin

Key ref:

S.Moréra et al. (1995). X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution. Structure, 3, 1307-1314. PubMed id: 8747457 DOI: 10.1016/S0969-2126(01)00268-4

Date:

06-Oct-95 Release date: 03-Apr-96

Protein chains

P22392  (NDKB_HUMAN) -  Nucleoside diphosphate kinase B

Seq: 152 a.a.

Struc: 151 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.7.13.3 - Histidine kinase.
• Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine

ATP + protein L-histidine = ADP (Bound ligand (Het Group name = GDP) matches with 96.00% similarity) + protein N-phospho-L-histidine

• Enzyme class 3: E.C.2.7.4.6 - Nucleoside-diphosphate kinase.
• Reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: ruffle (5 terms)
• Biological process: cell adhesion (18 terms)
• Biochemical function: nucleotide binding (9 terms)

reference

DOI no: 10.1016/S0969-2126(01)00268-4

Structure 3:1307-1314 (1995)

PubMed id: 8747457

X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution.

S.Moréra, M.L.Lacombe, Y.Xu, G.LeBras, J.Janin.

ABSTRACT

BACKGROUND: Nucleoside diphosphate (NDP) kinases provide precursors for DNA and RNA synthesis. In mammals, these enzymes are also involved in cell regulations. Human NDP kinase B, product of the human nm23-H2 gene, is both an enzyme and a transcription factor. It activates transcription of the c-myc oncogene independently of its catalytic function, by binding to its promoter DNA. How do the two functions coexist? RESULTS: Recombinant human NDP kinase B was co-crystallized with GDP. The X-ray structure was solved at 2.0 A resolution by molecular replacement from the homologous Drosophila Awd protein. Both enzymes are homo-hexamers with a characteristic beta alpha beta beta alpha beta fold. GDP binds near the active site His118. The guanine base is in a surface cleft and interacts with the C terminus of another subunit. CONCLUSIONS: The beta alpha beta beta alpha beta fold, also present in the 'palm' domain of Escherichia coli DNA polymerase I and HIV reverse transcriptase, is both a mononucleotide- and a polynucleotide-binding fold. If NDP kinase B binds DNA in the same way as the polymerases, the enzyme must undergo a conformation change in order to carry out gene activation.

Selected figure(s)

Figure 1.
Figure 1. . The NDP kinase B hexamer. (a) A view along the threefold axis. (b) View along a twofold axis in an orthogonal direction. α helices are in red and β strands are in blue. Helices α[1] and α[3] and the Kpn loops (yellow) form the core of the hexamer. The Kpn loops are at the poles of the molecule, near the threefold axis; helices α[A], α[2] and α[4], and the C-terminal extended segment are on the equator. Blue Van der Waals atoms represent bound GDP molecules. Figure 1. . The NDP kinase B hexamer. (a) A view along the threefold axis. (b) View along a twofold axis in an orthogonal direction. α helices are in red and β strands are in blue. Helices α[1] and α[3] and the Kpn loops (yellow) form the core of the hexamer. The Kpn loops are at the poles of the molecule, near the threefold axis; helices α[A], α[2] and α[4], and the C-terminal extended segment are on the equator. Blue Van der Waals atoms represent bound GDP molecules. (The figure was drawn with MOLSCRIPT [[4]38] with Raster3D [[5]39] rendering.)

Figure 3.
Figure 3. . Electron density for bound GDP. The F[o]–F[c] map is contoured at 2σ. Figure 3. . Electron density for bound GDP. The F[o]–F[c] map is contoured at 2σ. (The figure was drawn with TURBO, Drs A Roussel and C Cambillau, Marseille, France.)

The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 1307-1314) copyright 1995.

Figures were selected by an automated process.