2DI2

NMR structure of the HIV-2 nucleocapsid protein

Summary for 2DI2

• Entry DOI: 10.2210/pdb2di2/pdb
• Related: 1NC8
• Descriptor: Nucleocapsid protein p7, ZINC ION (2 entities in total)
• Functional Keywords: nucleocapsid protein, hiv-2, rna recognition, zinc finger, mutant, metal binding protein
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 3412.31

Authors

Matsui, T.,Kodera, Y.,Endoh, H.,Miyauchi, E.,Komatsu, H.,Sato, K.,Tanaka, T.,Kohno, T.,Maeda, T. (deposition date: 2006-03-27, release date: 2007-03-13, Last modification date: 2024-05-29)

Primary citation

Matsui, T.,Kodera, Y.,Endoh, H.,Miyauchi, E.,Komatsu, H.,Sato, K.,Tanaka, T.,Kohno, T.,Maeda, T.
RNA Recognition Mechanism of the Minimal Active Domain of the Human Immunodeficiency Virus Type-2 Nucleocapsid Protein
J.Biochem.(Tokyo), 141:269-277, 2007

PubMed Abstract: NCp8 of HIV-2 contains two CCHC-type zinc fingers connected by a linker, and is involved in many critical steps of the virus life cycle. It was previously shown that the first zinc finger flanked by the linker is the minimal active domain for specific binding to viral RNA. In our previous study, we determined the three-dimensional structure of NCp8-f1, including the minimal active domain, and found that a hydrogen bond between Asn(11) N(delta)H and Arg(27) O stabilized the conformation of the linker in the vicinity of the zinc finger [Kodera et al. (1998) Biochemistry 37, 17704-17713]. In this study, RNA binding activities of NCp8-f1 and three types of its mutant peptides were analysed by native PAGE assay. The activity and three-dimensional structure of NCp8-f1/N11A, in which alanine is substituted for Asn(11) thereby affecting the conformation of the linker, was analyzed and compared with those of NCp8-f1. We demonstrated that the existence of Arg(4) and/or Lys(5) and Arg(26) and/or Arg(27) were necessary for binding RNA. Furthermore, the linker's flexible orientation, which is controlled by the hydrogen bond between Asn(11) N(delta)H and Arg(27) O, appears to be a structural basis for NCp8 existing as a multi-functional protein.

PubMed: 17202191
DOI: 10.1093/jb/mvm037

Experimental method

SOLUTION NMR