PDBsum entry: 1nc8

Viral protein

PDB id: 1nc8

Contents

Protein chain

29 a.a.

Metals

_ZN

PDB id:

1nc8

Name:

Viral protein

Title:

High-resolution solution nmr structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein, 15 structures

Structure:

Nucleocapsid protein. Chain: a. Fragment: residues 1-29. Engineered: yes

Source:

Human immunodeficiency virus 2. Organism_taxid: 11709

NMR struc:

15 models

Authors:

Y.Kodera,K.Sato,T.Tsukahara,H.Komatsu,T.Maeda,T.Kohno

Key ref:

Y.Kodera et al. (1998). High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein. Biochemistry, 37, 17704-17713. PubMed id: 9922136 DOI: 10.1021/bi981818o

Date:

14-May-98 Release date: 25-May-99

Protein chain

P18042  (POL_HV2G1) -  Gag-Pol polyprotein

Seq: 1464 a.a.

Struc: 29 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
• Enzyme class 2: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
• Enzyme class 3: E.C.3.1.13.2 - Exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 4: E.C.3.1.26.13 - Retroviral ribonuclease H.
• Enzyme class 5: E.C.3.4.23.47 - HIV-2 retropepsin.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (2 terms)

reference

DOI no: 10.1021/bi981818o

Biochemistry 37:17704-17713 (1998)

PubMed id: 9922136

High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein.

Y.Kodera, K.Sato, T.Tsukahara, H.Komatsu, T.Maeda, T.Kohno.

ABSTRACT

The retroviral nucleocapsid (NC) protein is a multifunctional protein essential for RNA genome packaging and viral infectivity. The NC protein, NCp8, of the human immunodeficiency virus type-II (HIV-2) is a 49 amino acid peptide containing two zinc fingers, of the type C-X2-C-X4-H-X4-C, connected by seven amino acid residues, called the "basic amino acid cluster." It has been shown that the N-terminal zinc finger flanked by the basic amino acid cluster is the minimal active domain for the specific binding to viral RNA and other functions. However, the structure-activity relationships of NCp8 have not been investigated in detail. In the present study, the three-dimensional structure of a 29 amino acid peptide, including the minimal active domain (NCp8-fl), was determined by two-dimensional 1H NMR spectroscopy with simulated annealing calculations. A total of 15 converged structures of NCp8-fl were obtained on the basis of 355 experimental constraints, including 343 distance constraints obtained from nuclear Overhauser effect connectivities, 12 torsion angle (phi, chi1) constraints, and four constraints for zinc binding. The root-mean-square deviation of the 15 converged structures was 0.29 +/- 0.04 A for the backbone atoms (N, C(alpha), C) and 1.27 +/- 0.13 A for all heavy atoms. Interestingly, the basic amino acid cluster itself was defined well, with a loop-like conformation in which three arginine residues in the cluster and one arginine residue in the zinc finger are located approximately in the same plane of the molecule and are exposed to the solvent. The structure-activity relationships are discussed on the basis of the comparison of this well-defined structure with those of other NC proteins.