1NB2

Crystal Structure of Nucleoside Diphosphate Kinase from Bacillus Halodenitrificans

Summary for 1NB2

• Entry DOI: 10.2210/pdb1nb2/pdb
• Descriptor: Nucleoside Diphosphate Kinase (2 entities in total)
• Functional Keywords: nucleoside diphosphate kinase, bacillus halodenitrifians, transferase
• Biological source: Virgibacillus halodenitrificans
• Cellular location: Cytoplasm (By similarity): Q7SIA9
• Total number of polymer chains: 1
• Total formula weight: 14883.73

Authors

Chen, C.-J.,Liu, M.-Y.,Chang, W.-C.,Chang, T.,Wang, B.-C.,Le Gall, J. (deposition date: 2002-12-02, release date: 2003-05-06, Last modification date: 2024-03-13)

Primary citation

Chen, C.-J.,Liu, M.-Y.,Chang, T.,Chang, W.-C.,Wang, B.-C.,Le Gall, J.
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, 2003

PubMed 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.

PubMed: 12713952
DOI: 10.1016/S1047-8477(03)00014-5

Experimental method

X-RAY DIFFRACTION (2.2 Å)