4EVD

Crystal Structure HP-NAP from strain YS29 cadmium loaded (Cocrystallization 50mM)

Summary for 4EVD

• Entry DOI: 10.2210/pdb4evd/pdb
• Related: 3T9J 3TA8 4EVB 4EVC 4EVE
• Descriptor: Neutrophil-activating protein, CADMIUM ION (3 entities in total)
• Functional Keywords: dodecamer, four-helix bundle, metal transport
• Biological source: Helicobacter pylori
• Total number of polymer chains: 1
• Total formula weight: 20905.31

Authors

Yokoyama, H.,Tsuruta, O.,Akao, N.,Fujii, S. (deposition date: 2012-04-26, release date: 2012-06-27, Last modification date: 2023-11-08)

Primary citation

Yokoyama, H.,Tsuruta, O.,Akao, N.,Fujii, S.
Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form
Biochem.Biophys.Res.Commun., 422:745-750, 2012

PubMed Abstract: Helicobacter pylori neutrophil-activating protein (HP-NAP) is a Dps-like iron storage protein forming a dodecameric shell, and promotes adhesion of neutrophils to endothelial cells. The crystal structure of HP-NAP in a Zn(2+)- or Cd(2+)-bound form reveals the binding of two zinc or two cadmium ions and their bridged water molecule at the ferroxidase center (FOC). The two zinc ions are coordinated in a tetrahedral manner to the conserved residues among HP-NAP and Dps proteins. The two cadmium ions are coordinated in a trigonal-bipyramidal and distorted octahedral manner. In both structures, the second ion is more weakly coordinated than the first. Another zinc ion is found inside of the negatively-charged threefold-related pore, which is suitable for metal ions to pass through.

PubMed: 22618234
DOI: 10.1016/j.bbrc.2012.05.073

Experimental method

X-RAY DIFFRACTION (2.2 Å)