PDBsum entry 1ucn

Transferase

PDB id: 1ucn

Contents

Protein chains

151 a.a. *

Ligands

PO4 ×3

ADP ×3

TRS

Metals

_CA ×5

Waters ×336

* Residue conservation analysis

PDB id:

1ucn

Name:

Transferase

Title:

X-ray structure of human nucleoside diphosphate kinase a complexed with adp at 2 a resolution

Structure:

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

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.00Å R-factor: 0.237 R-free: 0.282

Authors:

Y.Chen,S.Gallois-Montbrun,B.Schneider,M.Veron,S.Morera,D.Deville- Bonne,J.Janin

Key ref:

Y.Chen et al. (2003). Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases. J Mol Biol, 332, 915-926. PubMed id: 12972261 DOI: 10.1016/j.jmb.2003.07.004

Date:

16-Apr-03 Release date: 30-Sep-03

Protein chains

P15531  (NDKA_HUMAN) -  Nucleoside diphosphate kinase A from Homo sapiens

Seq: 152 a.a.

Struc: 151 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.4.6 - nucleoside-diphosphate kinase.
• Reaction:
  1. a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP
  2. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP

ribonucleoside 5'-diphosphate + ATP = ribonucleoside 5'-triphosphate + ADP (Bound ligand (Het Group name = ADP) corresponds exactly)

2'-deoxyribonucleoside 5'-diphosphate + ATP = 2'-deoxyribonucleoside 5'-triphosphate + ADP (Bound ligand (Het Group name = ADP) corresponds exactly)

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

reference

DOI no: 10.1016/j.jmb.2003.07.004

J Mol Biol 332:915-926 (2003)

PubMed id: 12972261

Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases.

Y.Chen, S.Gallois-Montbrun, B.Schneider, M.Véron, S.Moréra, D.Deville-Bonne, J.Janin.

ABSTRACT

NDPK-A, product of the nm23-H1 gene, is one of the two major isoforms of human nucleoside diphosphate kinase. We analyzed the binding of its nucleotide substrates by fluorometric methods. The binding of nucleoside triphosphate (NTP) substrates was detected by following changes of the intrinsic fluorescence of the H118G/F60W variant, a mutant protein engineered for that purpose. Nucleoside diphosphate (NDP) substrate binding was measured by competition with a fluorescent derivative of ADP, following the fluorescence anisotropy of the derivative. We also determined an X-ray structure at 2.0A resolution of the variant NDPK-A in complex with ADP, Ca(2+) and inorganic phosphate, products of ATP hydrolysis. We compared the conformation of the bound nucleotide seen in this complex and the interactions it makes with the protein, with those of the nucleotide substrates, substrate analogues or inhibitors present in other NDP kinase structures. We also compared NDP kinase-bound nucleotides to ATP bound to protein kinases, and showed that the nucleoside monophosphate moieties have nearly identical conformations in spite of the very different protein environments. However, the beta and gamma-phosphate groups are differently positioned and oriented in the two types of kinases, and they bind metal ions with opposite chiralities. Thus, it should be possible to design nucleotide analogues that are good substrates of one type of kinase, and poor substrates or inhibitors of the other kind.

Selected figure(s)

Figure 4.
Figure 4. The nucleotide binding site of human NDPK-A. (A) ADP, Ca^2+ and inorganic phosphate bound to subunit A of H118G/F60W variant NDPK-A; the 2.0 Å resolution F[o]−F[c] electron density is contoured at 3σ. (B) Comparison of ADP-Pi-Ca^2+ in the variant NDPK-A (yellow bonds) with GDP-Mg^2+ bound to NDPK-B (green bonds). The two human NDP kinases are identical at their active site except for the H118G and F60W substitutions engineered in the variant. ADP and GDP interact with the same set of residues.

Figure 8.
Figure 8. The NTP environment and conformation in cAMP-dependent protein kinase and NDP kinase. ATP bound to cAPK (cAMP-dependent protein kinase,[46.] PDB entry 1ATP) is drawn in orange bonds. The triphosphate moiety interacts with the main-chain NH of residues 53-55, the side-chains of Lys72 and Lys168, and two Mn2+ labelled M1 and M2. ADP bound to the variant NDPK-A (yellow bonds) and R[p]-a-borano AZT triphosphate bound to a variant Dictyostelium NDP kinase[15.] (blue bonds, PDB entry 1MN7), are superimposed on ATP in cAPK. The AZT derivative binds the variant NDP kinase like the natural substrate dTTP; it carries a borano (BH[3]^ -) group in R[p] position of the a-phosphate. Mg2+ (blue ball) ligates the oxygen in the S[p] position, and the b and g-phosphate groups.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 332, 915-926) copyright 2003.

Figures were selected by an automated process.