PDBsum entry 1nb2

Transferase

PDB id: 1nb2

Contents

Protein chain

149 a.a. *

Waters ×34

* Residue conservation analysis

PDB id:

1nb2

Name:

Transferase

Title:

Crystal structure of nucleoside diphosphate kinase from bacillus halodenitrificans

Structure:

Nucleoside diphosphate kinase. Chain: a. Ec: 2.7.4.6

Source:

Virgibacillus halodenitrificans. Organism_taxid: 1482

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.20Å R-factor: 0.213 R-free: 0.254

Authors:

C.-J.Chen,M.-Y.Liu,W.-C.Chang,T.Chang,B.-C.Wang,J.Le Gall

Key ref:

C.J.Chen et al. (2003). Crystal structure of a nucleoside diphosphate kinase from Bacillus halodenitrificans: coexpression of its activity with a Mn-superoxide dismutase. J Struct Biol, 142, 247-255. PubMed id: 12713952 DOI: 10.1016/S1047-8477(03)00014-5

Date:

02-Dec-02 Release date: 06-May-03

Protein chain

Q7SIA9  (Q7SIA9_VIRHA) -  Nucleoside diphosphate kinase from Virgibacillus halodenitrificans

Seq: 150 a.a.

Struc: 149 a.a.

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

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

reference

DOI no: 10.1016/S1047-8477(03)00014-5

J Struct Biol 142:247-255 (2003)

PubMed id: 12713952

Crystal structure of a nucleoside diphosphate kinase from Bacillus halodenitrificans: coexpression of its activity with a Mn-superoxide dismutase.

C.J.Chen, M.Y.Liu, T.Chang, W.C.Chang, B.C.Wang, J.Le Gall.

ABSTRACT

We found that when grown under anaerobic conditions the moderate halophile, gram-positive bacterium Bacillus halodenitrificans (ATCC 49067) synthesizes large amounts of a polypeptide complex that contains a heme center capable of reversibly bind nitric oxide. This complex, when exposed to air, dissociates and reassociates into two active components, a Mn-containing superoxide dismutase (SOD) and a nucleoside diphosphate kinase (BhNDK). The crystal structure of this latter enzyme has been determined at 2.2A resolution using molecular replacement method, based on the crystal structure of Drosophila melanogaster NDK. The model contains 149 residues of a total 150 residues and 34 water molecules. BhNDK consists of a four-stranded antiparallel beta-sheet, whose surfaces are partially covered by six alpha-helices, and its overall and active site structures are similar to those of homologous enzymes. However, the hexameric packing of BhNDK shows that this enzyme is different from both eukaryotic and gram-negative bacteria. The need for the bacterium to presynthesize both SOD and NDK precursors which are activated during the anaerobic-aerobic transition is discussed.